Matlab

Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments...

AIM: The aim of work is to explore a quick, efficient, and effective patient-specific intensity-modulated radiation therapy (IMRT) quality assurance (QA). MATERIALS AND METHODS: Software tools were developed to extract and analyze the multi-leaf collimator (MLC) leaf positions (LPs) from electronic portal imaging device (EPID) images for Varian C-series machine and TrueBeam, to extract useful data from MLC log file of C-series linear accelerator (LINAC), to extract useful information from the trajectory log binary file of TrueBeam LINAC, to compare LPs derived from EPID images with log file/trajectory log data, and to analyze IMRT treatment files using the MATLAB programming language...

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Summary: Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently-labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly...

The successful implementation of the advanced sequencing technology, the next generation sequencing (NGS) motivates scientists from diverse fields of biological research especially from genomics and transcriptomics in generating large genomic data set to make their analysis more robust and come up with strong inference. However, exploiting this huge genomic data set becomes a challenge for the molecular biologists. To corroborate this problem, computational software and hardware are being developed in parallel and become an integral part of life science...

The induced dimerization of two distinct receptors through a heterobifunctional inducer is prevalent among all levels of cellular signaling processes, yet its complexity poses difficulty for systematic quantitative analysis. This paper first shows how to calculate the amount of any possible complex or monomer of heteroligand and two receptors present at equilibrium. The theory is subsequently applied to the determination of three independent equilibrium parameters involved in the rapamycin induced FKBP and FRB dimerization, in which all parameters were simultaneously estimated using one set of fluorescence resonance energy transfer (FRET) experiments...

Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs), and we then explain how to approximate DBN-based GRN models with continuous models. In addition, we show a MATLAB implementation of the key steps of this method, which we use to infer an Arabidopsis root GRN.

COmputation of Local Electron Release (COOLER), a software program designed for dosimetry assessment at the cellular/subcellular scale, with a given distribution of administered low-energy electron-emitting radionuclides in cellular compartments, which remains a critical step in risk/benefit analysis for advancements in internal radiotherapy. The software is intended to overcome the main limitations of the medical internal radiation dose (MIRD) formalism for calculations of cellular S-values (i.e., dose to a target region in the cell per decay in a given source region), namely, the use of the continuous slowing down approximation (CSDA) and the assumption of a spherical cell geometry...

Mathematical models of the cardiac cell have started to include markovian representations of the ionic channels instead of the traditional Hodgkin & Huxley formulations. There are many reasons for this: Markov models are not restricted to the idea of independent gates defining the channel, they allow more complex description with specific transitions between open, closed or inactivated states, and more importantly those states can be closely related to the underlying channel structure and conformational changes...

Hernia meshes significantly reduce recurrence rates in hernia repair. It's known that they affect the abdominal wall post-implantation, yet the understanding of in vivo mechanics in the mesh placement area is lacking. We established a single c-arm biplane fluoroscopic system to study strains at the interface between the mesh and repaired abdominal tissues. We aimed to validate this system for future porcine hernia repair studies. Custom MATLAB programs were written to correct for pincushion distortion, and direct linear transformation reconstructed objects in 3D...

In pelvic organ prolapse (POP), the organs are pushed downward along the lines of gravity, so measurements along this longitudinal body axis are desirable. We propose a universally applicable 3D coordinate system that corrects for changes in pelvic inclination and that allows the localization of any point in the pelvis at rest or under dynamic conditions on magnetic resonance images (MRI) of pelvic floor disorders in a scanner- and software independent manner. The proposed 3D coordinate system called 3D Pelvic Inclination Correction System (PICS) is constructed utilizing four bony landmark points, with the origin set at the inferior pubic point, and three additional points at the sacrum (sacrococcygeal joint) and both ischial spines, which are clearly visible on MRI images...

OBJECTIVES: To retrospectively evaluate the diagnostic value of high-frequency power (HFP) compared with the minimum apparent diffusion coefficient (MinADC) in the prediction of neuroepithelial tumour grading. METHODS: Diffusion-weighted imaging (DWI) data were acquired on 115 patients by a 3.0-T MRI system, which included b0 images and b1000 images over the whole brain in each patient. The HFP values and MinADC values were calculated by an in-house script written on the MATLAB platform...

INTRODUCTION: In radiotherapy, megaelectron volt (MeV) electrons are employed for treatment of superficial cancers. Magnetic fields can be used for deflection and deformation of the electron flow. A magnetic field is composed of non-uniform permanent magnets. The primary electrons are not mono-energetic and completely parallel. Calculation of electron beam deflection requires using complex mathematical methods. In this study, a device was made to apply a magnetic field to an electron beam and the path of electrons was simulated in the magnetic field using finite element method...

The situation of missing children is one of the most emotional social issues worldwide. The search for and identification of missing children is often hampered, among others, by the fact that the facial morphology of long-term missing children changes as they grow. Nowadays, the wide coverage by surveillance systems potentially provides image material for comparisons with images of missing children that may facilitate identification. The aim of study was to identify whether facial features are stable in time and can be utilized for facial recognition by comparing facial images of children at different ages as well as to test the possible use of moles in recognition...

PURPOSE: To implement an aggregation method in Matlab for generating ActiGraph counts from raw acceleration recorded with an alternative accelerometer device and to investigate the validity of the method. METHODS: The aggregation method including the frequency band-pass filter was implemented and optimized based on standardized sinusoidal acceleration signals generated in Matlab and processed in the ActiLife software. Evaluating the validity of the aggregation method was approached using a mechanical setup and with a 24-hour free-living recording using a convenient sample of nine subjects...

OBJECTIVE: In achalasia, absent peristalsis and reduced esophagogastric junction (EGJ) relaxation and compliance underlie dysphagia symptoms. Novel high-resolution impedance manometry (HRIM) variables, i.e. bolus presence time (BPT) and trans-EGJ-bolus flow time (BFT) have been developed to estimate the duration of EGJ opening and trans-EGJ bolus flow. The aim of this study was to evaluate esophageal motor function and bolus flow in children diagnosed with achalasia using these variables...

PURPOSE: Commonly 2D scouts or topograms are used prior to CT scan acquisition. However, low-dose 3D scouts could potentially provide additional information for more effective patient positioning and selection of acquisition protocols. We propose using model-based iterative reconstruction to reconstruct low exposure tomographic data to maintain image quality in both low-dose 3D scouts and reprojected topograms based on those 3D scouts. METHODS: We performed tomographic acquisitions on a CBCT test-bench using a range of exposure settings from 16...

We demonstrate an application of atomic force microscopy (AFM) for the structural analysis of long single-stranded RNA (>1 kb), focusing on 28S ribosomal RNA (rRNA). Generally, optimization of the conditions required to obtain three-dimensional (3D) structures of long RNA molecules is a challenging or nearly impossible process. In this study, we overcome these limitations by developing a method using AFM imaging combined with automated, MATLAB-based image analysis algorithms for extracting information about the domain organization of single RNA molecules...

BACKGROUND: Loss of thoracic kyphosis has been associated with thoracic idiopathic scoliosis. Modern 3-dimensional (3D) imaging systems allow more accurate characterization of the scoliotic deformity than traditional radiographs. In this study, we utilized 3D calculations to characterize the association between increasing scoliosis severity and changes in the sagittal and axial planes. METHODS: Patients evaluated in a scoliosis clinic and determined to have either a normal spine or idiopathic scoliosis were included in the analysis...

This project aims to develop a novel large stroke asymmetric pneumatic servo system of a hardware-in-the-loop for path tracking control under variable loads based on the MATLAB Simulink real-time system. High pressure compressed air provided by the air compressor is utilized for the pneumatic proportional servo valve to drive the large stroke asymmetric rod-less pneumatic actuator. Due to the pressure differences between two chambers, the pneumatic actuator will operate. The highly nonlinear mathematical models of the large stroke asymmetric pneumatic system were analyzed and developed...