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https://www.readbyqxmd.com/read/28934238/a-tool-to-automatically-analyze-electromagnetic-tracking-data-from-high-dose-rate-brachytherapy-of-breast-cancer-patients
#1
Th I Götz, G Lahmer, V Strnad, Ch Bert, B Hensel, A M Tomé, E W Lang
During High Dose Rate Brachytherapy (HDR-BT) the spatial position of the radiation source inside catheters implanted into a female breast is determined via electromagnetic tracking (EMT). Dwell positions and dwell times of the radiation source are established, relative to the patient's anatomy, from an initial X-ray-CT-image. During the irradiation treatment, catheter displacements can occur due to patient movements. The current study develops an automatic analysis tool of EMT data sets recorded with a solenoid sensor to assure concordance of the source movement with the treatment plan...
2017: PloS One
https://www.readbyqxmd.com/read/28917015/metronome-lkm-an-open-source-virtual-keyboard-driver-to-measure-experiment-software-latencies
#2
Pablo Garaizar, Miguel A Vadillo
Experiment software is often used to measure reaction times gathered with keyboards or other input devices. In previous studies, the accuracy and precision of time stamps has been assessed through several means: (a) generating accurate square wave signals from an external device connected to the parallel port of the computer running the experiment software, (b) triggering the typematic repeat feature of some keyboards to get an evenly separated series of keypress events, or (c) using a solenoid handled by a microcontroller to press the input device (keyboard, mouse button, touch screen) that will be used in the experimental setup...
September 15, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28880154/micromagnetic-stimulation-of-the-mouse-auditory-cortex-in-vivo-using-an-implantable-solenoid-system
#3
Shunsuke Minusa, Hisayuki Osanai, Takashi Tateno
OBJECTIVE: Recent studies have reported that micromagnetic stimulation (μMS), which can activate neural tissue and cells via sub-millimeter inductors, may address several limitations of conventional magnetic stimulation methods. Previous studies have examined the effects of μMS on single neurons, yet little is known about how μMS can affect brain tissue including local neural networks. Here, we propose a new, readily available implantable μMS system and computationally and experimentally evaluate its validity...
September 1, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28855255/single-molecule-force-spectroscopy-on-histone-h4-tail-cross-linked-chromatin-reveals-fiber-folding
#4
Artur Kaczmarczyk, Abdollah Allahverdi, Thomas B Brouwer, Lars Nordenskiöld, Nynke H Dekker, John van Noort
The eukaryotic genome is highly compacted into a protein-DNA complex called chromatin. The cell controls access of transcriptional regulators to chromosomal DNA via several mechanisms that act on chromatin-associated proteins and provide a rich spectrum of epigenetic regulation. Elucidating the mechanisms that fold chromatin fibers into higher-order structures is therefore key to understanding the epigenetic regulation of DNA accessibility. Here, using histone H4-V21C and histone H2A-E64C mutations, we employed single-molecule force spectroscopy to measure the unfolding of individual chromatin fibers that are reversibly cross-linked through the histone H4 tail...
August 30, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28840859/cryo-em-structure-of-human-dna-pk-holoenzyme
#5
Xiaotong Yin, Mengjie Liu, Yuan Tian, Jiawei Wang, Yanhui Xu
DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ), the major DNA repair pathway. Here, we determined cryo-electron microscopy structure of human DNA-PK holoenzyme at 6.6 Å resolution. In the complex structure, DNA-PKcs, KU70, KU80 and DNA duplex form a 650-kDa heterotetramer with 1:1:1:1 stoichiometry. The N-terminal α-solenoid (∼2 800 residues) of DNA-PKcs adopts a double-ring fold and connects the catalytic core domain of DNA-PKcs and KU70/80-DNA...
August 25, 2017: Cell Research
https://www.readbyqxmd.com/read/28838667/the-structure-of-the-infectious-prion-protein-and-its-propagation
#6
Jesús R Requena, Holger Wille
The prion diseases, which include Creutzfeldt-Jakob disease in humans, chronic wasting disease in cervids (i.e., deer, elk, moose, and reindeer), bovine spongiform encephalopathy in cattle, as well as sheep and goat scrapie, are caused by the conversion of the cellular prion protein (PrP(C)) into a disease-causing conformer (PrP(Sc)). PrP(C) is a regular, GPI-anchored protein that is expressed on the cell surface of neurons and many other cell types. The structure of PrP(C) is well studied, based on analyses of recombinant PrP, which is thought to mimic the structure of native PrP(C)...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28822304/a-flow-through-elevated-temperature-and-pressure-nmr-apparatus-for-in-situ-co2-sequestration-studies
#7
Erika L Sesti, Jinlei Cui, Sophia E Hayes, Mark S Conradi
We report an apparatus for in-situ nuclear magnetic resonance (NMR) studies of chemical reactions of dissolved (13)CO2 with minerals (rock or powder) under continuous flow. The operating range of the apparatus is 18-150°C and 1-140bar. A flow pump is used to circulate a CO2-water solution, with a heated mixing vessel where CO2 gas equilibrates with a water solution. The NMR probe is built around a strong zirconia ceramic vessel, with o-ring sealed connections; the mineral is contained inside. The horizontal orientation of the zirconia vessels allows use of a radio frequency (rf) solenoid for improved spin sensitivity...
August 12, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28806939/effect-of-electromagnetic-fields-on-human-osteoarthritic-and-non-osteoarthritic-chondrocytes
#8
Julia Isabelle Redeker, Bärbel Schmitt, Nele Pascale Grigull, Christian Braun, Andreas Büttner, Volkmar Jansson, Susanne Mayer-Wagner
BACKGROUND: Studies of the effects of electromagnetic fields (EMFs) on cartilaginous cells show a broad range of outcomes. However EMFs are not yet clinically applied as standard treatment of osteoarthritis, as EMF effects are showing varying outcomes in the literature. The aim of this study was to examine effects of EMFs (5 mT or 8 mT) on osteoarthritic (OA) and non-OA chondrocytes in order to investigate whether EMF effects are related to chondrocyte and EMF quality. METHODS: Pellets of human OA and non-OA chondrocytes were exposed to a sinusoidal 15 Hz EMF produced by a solenoid...
August 14, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28805224/molecular-dynamics-based-strength-estimates-of-beta-solenoid-proteins
#9
Amanda Parker, Krishnakumar Ravikumar, Daniel Cox
The use of beta solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their mechanical strengths, we can efficiently design the proteins for specific functions. We present a study of the mechanical properties of seven beta solenoid proteins using GROMACS molecular dynamics software to produce force/torque-displacement data, implement umbrella sampling of bending/twisting trajectories, produce Potentials of Mean Force (PMFs), extract effective spring constants, and calculate rigidities for two bending and two twisting directions for each protein...
September 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28801909/promoter-activation-with-electromagnetism
#10
Abraham O Rodríguez-De la Fuente, J Antonio Heredia-Rojas, Juan M Alcocer-González, Laura E Rodríguez-Flores, Cristina Rodríguez-Padilla, Reyes S Taméz-Guerra
Gene expression can be modified by physical factors, such as heat, electricity and magnetic fields , and several types of ionizing and non-ionizing radiation. Promoter activation with extremely low-frequency electromagnetic fields is possible with an appropriate promoter, containing electromagnetic field response elements. Here, we describe how to examine promoter activation with extremely low-frequency electromagnetic fields, and we provide a step-by-step guide to the assembly of a solenoid suitable for promoter activation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28796645/on-the-use-of-particle-filters-for-electromagnetic-tracking-in-high-dose-rate-brachytherapy
#11
Theresa Ida Götz, Godehard Lahmer, Tobias Brandt, Karoline Kallis, Vratislav Strnad, Christoph Bert, Bernhard Hensel, Ana Maria Tome, Elmar W Lang
Modern radiotherapy of female breat cancers often employ high dose rate Brachytherapy, where a radioactive source is moved inside catheters, implanted in the female breast, according to a prescribed treatment plan. Source localization relative to the patient's anatomy is determined with solenoid sensors whose spatial positions are measured with an electromagnetic tracking system. Precise sensor dwell position determination is of utmost importance to assure irradiation of the cancerous tissue according to the treatment plan...
August 10, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28792846/nanodosimetric-simulation-of-direct-ion-induced-dna-damage-using-different-chromatin-geometry-models
#12
N T Henthorn, J W Warmenhoven, M Sotiropoulos, R I Mackay, K J Kirkby, M J Merchant
Monte Carlo based simulation has proven useful in investigating the effect of proton-induced DNA damage and the processes through which this damage occurs. Clustering of ionizations within a small volume can be related to DNA damage through the principles of nanodosimetry. For simulation, it is standard to construct a small volume of water and determine spatial clusters. More recently, realistic DNA geometries have been used, tracking energy depositions within DNA backbone volumes. Traditionally a chromatin fiber is built within the simulation and identically replicated throughout a cell nucleus, representing the cell in interphase...
August 9, 2017: Radiation Research
https://www.readbyqxmd.com/read/28789542/intracavity-faraday-modulation-spectroscopy-infamos-a-tool-for-radical-detection
#13
Michele Gianella, Tomas H P Pinto, Xia Wu, Grant A D Ritchie
We present the intra-cavity Faraday modulation spectroscopy technique, whereby optical feedback cavity-enhanced spectroscopy is coupled with Faraday modulation spectroscopy to greatly enhance the interaction path length of a laser beam with a paramagnetic sample in a magnetic field. We describe a first prototype based upon a cw quantum cascade laser targeting a selection of fundamental rovibrational R-branch transitions of nitric oxide (1890 cm(-1)), consisting of a linear cavity (finesse F=6300) and a water-cooled solenoid...
August 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28767037/cryo-em-structure-of-the-saga-and-nua4-coactivator-subunit-tra1-at-3-7-angstrom-resolution
#14
Luis Miguel Díaz-Santín, Natasha Lukoyanova, Emir Aciyan, Alan Cm Cheung
Coactivator complexes SAGA and NuA4 stimulate transcription by post-translationally modifying chromatin. Both complexes contain the Tra1 subunit, a highly conserved 3744-residue protein from the Phosphoinositide 3-Kinase-related kinase (PIKK) family and a direct target for multiple sequence-specific activators. We present the Cryo-EM structure of Saccharomyces cerevsisae Tra1 to 3.7 Å resolution, revealing an extensive network of alpha-helical solenoids organized into a diamond ring conformation and is strikingly reminiscent of DNA-PKcs, suggesting a direct role for Tra1 in DNA repair...
August 2, 2017: ELife
https://www.readbyqxmd.com/read/28731757/phase-locking-the-spin-precession-in-a-storage-ring
#15
N Hempelmann, V Hejny, J Pretz, E Stephenson, W Augustyniak, Z Bagdasarian, M Bai, L Barion, M Berz, S Chekmenev, G Ciullo, S Dymov, F-J Etzkorn, D Eversmann, M Gaisser, R Gebel, K Grigoryev, D Grzonka, G Guidoboni, T Hanraths, D Heberling, J Hetzel, F Hinder, A Kacharava, V Kamerdzhiev, I Keshelashvili, I Koop, A Kulikov, A Lehrach, P Lenisa, N Lomidze, B Lorentz, P Maanen, G Macharashvili, A Magiera, D Mchedlishvili, S Mey, F Müller, A Nass, N N Nikolaev, A Pesce, D Prasuhn, F Rathmann, M Rosenthal, A Saleev, V Schmidt, Y Semertzidis, V Shmakova, A Silenko, J Slim, H Soltner, A Stahl, R Stassen, H Stockhorst, H Ströher, M Tabidze, G Tagliente, R Talman, P Thörngren Engblom, F Trinkel, Yu Uzikov, Yu Valdau, E Valetov, A Vassiliev, C Weidemann, A Wrońska, P Wüstner, P Zuprański, M Żurek
This Letter reports the successful use of feedback from a spin polarization measurement to the revolution frequency of a 0.97  GeV/c bunched and polarized deuteron beam in the Cooler Synchrotron (COSY) storage ring in order to control both the precession rate (≈121  kHz) and the phase of the horizontal polarization component. Real time synchronization with a radio frequency (rf) solenoid made possible the rotation of the polarization out of the horizontal plane, yielding a demonstration of the feedback method to manipulate the polarization...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28706244/predicting-magnetostimulation-thresholds-in-the-peripheral-nervous-system-using-realistic-body-models
#16
Mathias Davids, Bastien Guérin, Matthias Malzacher, Lothar R Schad, Lawrence L Wald
Rapid switching of applied magnetic fields in the kilohertz frequency range in the human body induces electric fields powerful enough to cause Peripheral Nerve Stimulation (PNS). PNS has become one of the main constraints on the use of high gradient fields for fast imaging with the latest MRI gradient technology. In recent MRI gradients, the applied fields are powerful enough that PNS limits their application in fast imaging sequences like echo-planar imaging. Application of Magnetic Particle Imaging (MPI) to humans is similarly PNS constrained...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28691351/structures-of-designed-armadillo-repeat-proteins-binding-to-peptides-fused-to-globular-domains
#17
Simon Hansen, Jonathan D Kiefer, Chaithanya Madhurantakam, Peer R E Mittl, Andreas Plückthun
Designed armadillo repeat proteins (dArmRP) are α-helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term "peptide" not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops, or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N-terminus of Green Fluorescent Protein or to the C-terminus of a phage lambda protein D...
October 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28685470/construction-of-0-15-tesla-overhauser-enhanced-mri
#18
Yuumi Tokunaga, Motonao Nakao, Tatsuya Naganuma, Kazuhiro Ichikawa
Overhauser enhanced MRI (OMRI) is one of the free radical imaging technologies and has been used in biomedical research such as for partial oxygen measurements in tumor, and redox status in acute oxidative diseases. The external magnetic field of OMRI is frequently in the range of 5-10 mTesla to ensure microwave penetration into small animals, and the S/N ratio is limited. In this study, a 0.15 Tesla OMRI was constructed and tested to improve the S/N ratio for a small sample, or skin measurement. Specification of the main magnet was as follows: 0...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28673961/understanding-the-molecular-differential-recognition-of-muramyl-peptide-ligands-by-lrr-domains-of-human-nod-receptors
#19
Sukhithasri Vijayrajratnam, Anju Choorakottayil Pushkaran, Aathira Balakrishnan, Anil Kumar Vasudevan, Raja Biswas, Chethampadi Gopi Mohan
Human nucleotide-binding oligomerization domain proteins, hNOD1 and hNOD2, are host intracellular receptors with C-terminal leucine-rich repeat (LRR) domains, which recognize specific bacterial peptidoglycan (PG) fragments as their ligands. The specificity of this recognition is dependent on the third amino acid of the stem peptide of the PG ligand, which is usually meso-diaminopimelic acid (mesoDAP) or l-lysine (l-Lys). Since the LRR domains of hNOD receptors had been experimentally shown to confer the PG ligand-sensing specificity, we developed three-dimensional structures of hNOD1-LRR and the hNOD2-LRR to understand the mechanism of differential recognition of muramyl peptide ligands by hNOD receptors...
July 27, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28663553/functional-and-dynamic-polymerization-of-the-als-linked-protein-tdp-43-antagonizes-its-pathologic-aggregation
#20
Tariq Afroz, Eva-Maria Hock, Patrick Ernst, Chiara Foglieni, Melanie Jambeau, Larissa A B Gilhespy, Florent Laferriere, Zuzanna Maniecka, Andreas Plückthun, Peer Mittl, Paolo Paganetti, Frédéric H T Allain, Magdalini Polymenidou
TDP-43 is a primarily nuclear RNA-binding protein, whose abnormal phosphorylation and cytoplasmic aggregation characterizes affected neurons in patients with amyotrophic lateral sclerosis and frontotemporal dementia. Here, we report that physiological nuclear TDP-43 in mouse and human brain forms homo-oligomers that are resistant to cellular stress. Physiological TDP-43 oligomerization is mediated by its N-terminal domain, which can adopt dynamic, solenoid-like structures, as revealed by a 2.1 Å crystal structure in combination with nuclear magnetic resonance spectroscopy and electron microscopy...
June 29, 2017: Nature Communications
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