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Karolina Kwasek, Simona Rimoldi, Anna Giulia Cattaneo, Timothy Parker, Konrad Dabrowski, Genciana Terova
Hypoxia can affect various fish populations, including yellow perch Perca flavescens, which is an economically and ecologically important species in Lake Erie, a freshwater system that often experiences hypoxia in the hypolimnetic part of the lake. Fish, similarly to mammals, possess molecular oxygen sensor-hypoxia-inducible factor-1 (HIF-1), a transcription factor that can affect expression of many downstream genes related to animal growth and locomotion, protein synthesis, as well as ATP and amino acid metabolism...
January 18, 2017: Fish Physiology and Biochemistry
Pauli Parkkinen, Sergio A Losilla, Eelis Solala, Elias A Toivanen, Wen-Hua Xu, Dage Sundholm
A grid-based fast multipole method (GB-FMM) for optimizing three-dimensional (3D) numerical molecular orbitals in the dual bubbles and cube basis has been developed and implemented. The present GB-FMM method is a generalization of our recently published GB-FMM approach for numerically calculating electrostatic potentials and two-electron interaction energies. The orbital optimization is performed by integrating the Helmholtz kernel in the dual basis. The steep part of the functions in the vicinity of the nuclei is represented by one-center bubbles functions, whereas the remaining cube part is expanded on an equidistant 3D grid...
January 17, 2017: Journal of Chemical Theory and Computation
Pengfei Li, Glen P Jackson
1+, 2+, and 3+ precursors of substance P and bradykinin were subjected to helium cation irradiation in a 3D ion trap mass spectrometer. Charge exchange with the helium cations produces a variety of fragment ions, the number and type of which are dependent on the charge state of the precursor ions. For 1+ peptide precursors, fragmentation is generally restricted to C-CO backbone bonds (a and x ions), whereas for 2+ and 3+ peptide precursors, all three backbone bonds (C-CO, C-N, and N-Cα) are cleaved. The type of backbone bond cleavage is indicative of possible dissociation channels involved in CTD process, including high-energy, kinetic-based, and ETD-like pathways...
January 13, 2017: Journal of the American Society for Mass Spectrometry
A Oines, A Oines, J Kilian-Meneghin, B Karthikeyan, S Rudin, D Bednarek
PURPOSE: The Dose Tracking System (DTS) was developed to provide realtime feedback of skin dose and dose rate during interventional fluoroscopic procedures. A color map on a 3D graphic of the patient represents the cumulative dose distribution on the skin. Automated image correlation algorithms are described which use the fluoroscopic procedure images to align and scale the patient graphic for more accurate dose mapping. METHODS: Currently, the DTS employs manual patient graphic selection and alignment...
June 2016: Medical Physics
D Matenine, G Cote, J Mascolo-Fortin, Y Goussard, P Despres
PURPOSE: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons' trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. METHODS: We propose an optimized implementation of the Siddon's algorithm using graphics processing units (GPUs) with a novel data storage scheme...
June 2016: Medical Physics
V Gutti, A Morrow, S Kim, M Patel
PURPOSE: Stereotactic radiosurgery (SRS) treatments using conical collimators can potentially result in gantry collision with treatment table due to limited collision-clear spaces. An in-house software was developed to help the SRS treatment planner mitigate potential SRS conical collimator (Varian Medical System, Palo Alto, CA) collisions with the treatment table. This software was designed to remove treatment re-planning secondary to unexpected collisions. METHODS: A BrainLAB SRS ICT Frameless Extension used for SRS treatments in our clinic was mathematically modelled using surface points registered to the 3D co-ordinate space of the couch extension...
June 2016: Medical Physics
S Jiang, S Dolly, B Cai, S Mutic, H Li
PURPOSE: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. METHODS: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors...
June 2016: Medical Physics
S Vijayan, Z Xiong, A Shankar, S Rudin, D Bednarek
PURPOSE: To determine the distribution of backscattered radiation to the skin resulting from a non-uniform distribution of primary radiation through convolution with a backscatter point spread function (PSF). METHODS: A backscatter PSF is determined using Monte Carlo simulation of a 1 mm primary beam incident on a 30 × 30 cm × 20 cm thick PMMA phantom using EGSnrc software. A primary profile is similarly obtained without the phantom and the difference from the total provides the backscatter profile...
June 2016: Medical Physics
Ingo Heimbach, Florian Rhiem, Fabian Beule, David Knodt, Josef Heinen, Robert O Jones
pyMolDyn is an interactive viewer of atomic systems defined in a unit cell and is particularly useful for crystalline and amorphous materials. It identifies and visualizes cavities (vacancies, voids) in simulation cells corresponding to all seven 3D Bravais lattices, makes no assumptions about cavity shapes, allows for atoms of different size, and locates the cavity centers (the centers of the largest spheres not including an atom center). We define three types of cavity and develop a method based on the split and merge algorithm to calculate all three...
March 5, 2017: Journal of Computational Chemistry
José Morales-Roselló, Asma Khalil, Victoria Fornes Ferrer, David Hervas-Marín, Nuria Peralta Llorens, Juan Rubio Moll, Alfredo Perales-Marín
OBJECTIVE: Low cerebroplacental ratio (CPR) near term has emerged as a marker of fetal adverse outcome. The aim of this study was to evaluate the predictive accuracy of an alternative ratio using the vertebral artery (vertebroplacental ratio or VPR) for acid-base status at birth. METHODS: This was a prospective cohort study of 1470 pregnancies undergoing an ultrasound assessment of the umbilical artery, middle cerebral artery and vertebral artery Doppler beyond 34 weeks' gestation within 14 days of delivery...
December 27, 2016: Journal of Maternal-fetal & Neonatal Medicine
Sébastien A A Gros, William Xu, John C Roeske, Mehe Choi, Bahman Emami, Murat Surucu
To develop a novel method to monitor external anatomical changes in head and neck cancer patients in order to triage possible adaptive radiotherapy needs METHODS: The presented approach aims to provide information on internal anatomical changes based on variations observed in external anatomy. Setup Cone Beam Computed Tomography (CBCT) images are processed to produce an accurate external contour of the patient's skin. After registering the CBCTs to the reference planning CT, the external contours from each CBCT are transferred to the initial- first week - CBCT...
December 26, 2016: Medical Physics
Estelle Jean Dit Gautier, Virginie Bot-Robin, Aurélien Libessart, Guillaume Doucède, Michel Cosson, Chrystèle Rubod
BACKGROUND: The emergence of new technologies in the obstetrical field should lead to the development of learning applications, specifically for obstetrical emergencies. Many childbirth simulations have been recently developed. However, to date none of them have been integrated into a serious game. OBJECTIVE: Our objective was to design a new type of immersive serious game, using virtual glasses to facilitate the learning of pregnancy and childbirth pathologies...
December 21, 2016: JMIR Serious Games
Eduardo Castanon, Sandrine Aspeslagh, Jean-Charles Soria
No abstract text is available yet for this article.
December 19, 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
Jitendra Kumar, Tarana Umar, Tasneem Kausar, Mohammad Mobashir, Shahid M Nayeem, Nasimul Hoda
The phosphodiesterase (PDE) family of proteins are important regulators of signal transduction, which they achieve by controlling the secondary messengers cyclic AMP (cAMP) and cyclic GMP (cGMP). cAMP and cGMP are involved in many critical intracellular processes such as gene transcription, kinase activation, signal transduction in learning and memory, and channel function as secondary messengers. The involvement of PDEs in neuronal communication has made them important therapeutic targets. Considering the recent discovery that PDE2A inhibition can improve cognitive functioning, a combined molecular dynamics simulation and scoring and docking study was carried out to identify selective inhibitors of PDE2A that specifically interact with the recently discovered hydrophobic groove in PDE2A...
January 2017: Journal of Molecular Modeling
Yuichi Kano, Prachya Musikasinthorn, Akihisa Iwata, Sein Tun, Lkc Yun, Seint Seint Win, Shoko Matsui, Ryoichi Tabata, Takeshi Yamasaki, Katsutoshi Watanabe
BACKGROUND: Inle (Inlay) Lake, an ancient lake of Southeast Asia, is located at the eastern part of Myanmar, surrounded by the Shan Mountains. Detailed information on fish fauna in and around the lake has long been unknown, although its outstanding endemism was reported a century ago. NEW INFORMATION: Based on the fish specimens collected from markets, rivers, swamps, ponds and ditches around Inle Lake as well as from the lake itself from 2014 to 2016, we recorded a total of 948 occurrence data (2120 individuals), belonging to 10 orders, 19 families, 39 genera and 49 species...
2016: Biodiversity Data Journal
Dan MacDougall, Joshua Farrell, Jeremy Brown, Manohar Bance, Robert Adamson
We present the design, implementation and validation of a swept-source optical coherence tomography (OCT) system for real-time imaging of the human middle ear in live patients. Our system consists of a highly phase-stable Vernier-tuned distributed Bragg-reflector laser along with a real-time processing engine implemented on a graphics processing unit. We use the system to demonstrate, for the first time in live subjects, real-time Doppler measurements of middle ear vibration in response to sound, video rate 2D B-mode imaging of the middle ear and 3D volumetric B-mode imaging...
November 1, 2016: Biomedical Optics Express
Mikoláš Jurda, Petra Urbanová
The present paper aims to test performances of semi-automatic tools for mesh-to-mesh processing while assessing sex and ancestry in documented human crania. The studied sample of 80 human crania, which originated in two documented Brazilian collections (São Paulo, Brazil) was digitized using photogrammetry and laser scanning. 3D cranial morphology was quantified by computing inter-mesh dissimilarity measures using in-house freeware FIDENTIS Analyst ( Numerical outputs were further processed using Discriminant Function Analysis and Canonical Variant Analysis in order to classify models into sex and ancestry groups...
November 2016: Legal Medicine
Deborah Jarvis, Rahim Akram, Laura Mandefield, Michael Paddock, Paul Armitage, Paul D Griffiths
OBJECTIVE: Interpretation of magnetic resonance (MR) imaging of the fetal brain in utero is primarily undertaken using 2D images to provide anatomical information about structural abnormalities. It is now possible to obtain 3D image acquisitions that allow measurement of fetal brain volumes that are potentially useful clinically. The aim of our current work is to provide reference values of total brain volumes obtained from a cohort of low risk fetuses with no abnormalities on ante-natal ultrasonography and in utero MR imaging...
December 2016: Prenatal Diagnosis
Luca Cevenini, Maria Maddalena Calabretta, Antonia Lopreside, Giuseppe Tarantino, Annalisa Tassoni, Maura Ferri, Aldo Roda, Elisa Michelini
The availability of smartphones with high-performance digital image sensors and processing power has completely reshaped the landscape of point-of-need analysis. Thanks to the high maturity level of reporter gene technology and the availability of several bioluminescent proteins with improved features, we were able to develop a bioluminescence smartphone-based biosensing platform exploiting the highly sensitive NanoLuc luciferase as reporter. A 3D-printed smartphone-integrated cell biosensor based on genetically engineered Hek293T cells was developed...
December 2016: Analytical and Bioanalytical Chemistry
Varun Arora, Richard Hannan, Richard Beaver, Timothy Fletcher, Paul Harvie
OBJECTIVE: The aim was to develop a CT-based protocol to accurately measure post-operative acetabular cup inclination and anteversion establishing which bony reference points facilitate the most accurate estimation of these variables. MATERIALS AND METHODS: An all-polyethylene acetabular liner was implanted into a cadaveric acetabulum. A conventional pelvic CT scan was performed and reformatted images created in both functional and anterior pelvic planes. CT images were transferred to a Freedom-Plus Graphics software package enabling an identical, virtual 3D model of the cadaveric pelvis to be created and definitive acetabular cup orientation established...
February 2017: Skeletal Radiology
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