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Kurtis H Dekker, Rubin Hazarika, Matheus A Silveira, Kevin J Jordan
Optical cone beam computed tomography (CT) scanning of radiochromic gel dosimeters, using a CCD camera and a low stray light convergent source, provides fast, truly 3D radiation dosimetry with high accuracy. However, a key limiting factor in radiochromic gel dosimetry at large (⩾10 cm diameter) volumes is the initial attenuation of the dosimeters. It is not unusual to observe a 5-10×  difference in signal intensity through the dosimeter center versus through the surrounding medium in pre-irradiation images...
March 16, 2018: Physics in Medicine and Biology
Adam Wang, Alexander Maslowski, Philippe Messmer, Mathias Lehmann, Adam Strzelecki, Elaine Yu, Pascal Paysan, Marcus Brehm, Peter Munro, Josh Star-Lack, Dieter Seghers
PURPOSE: To correct for scatter in kV cone-beam CT (CBCT) projection data on a clinical system using a new tool, Acuros® CTS, that estimates scatter images rapidly and accurately by deterministically solving the linear Boltzmann transport equation. METHODS: Phantom and patient CBCT scans were acquired on TrueBeam® radiotherapy machines. A first-pass reconstruction was used to create water and bone density maps of the imaged object, which was updated to include a more accurate representation of the patient couch...
March 6, 2018: Medical Physics
Alexander Maslowski, Adam Wang, Mingshan Sun, Todd Wareing, Ian Davis, Josh Star-Lack
PURPOSE: To describe Acuros® CTS, a new software tool for rapidly and accurately estimating scatter in x-ray projection images by deterministically solving the linear Boltzmann transport equation (LBTE). METHODS: The LBTE describes the behavior of particles as they interact with an object across spatial, energy, and directional (propagation) domains. Acuros CTS deterministically solves the LBTE by modeling photon transport associated with an x-ray projection in three main steps: 1) Ray tracing photons from the x-ray source into the object where they experience their first scattering event and form scattering sources...
March 6, 2018: Medical Physics
C Yamauchi-Kawaura, S Yamamoto, K Fujii, M Komori, M Yamauchi, N Ohzawa, M Kozuka, N Suga, N Ito, A Fukuyama
This study proposes a new dosimetry method for the estimation of the internal radiation dose distribution of a subject undergoing computed tomography (CT) examinations. In this novel method, dose distribution of a subject by CT scans was estimated based on radiophotoluminance distribution with polyethylene terephthalate (PET) resin which was cut to the average head size of a Japanese 1-year-old child. The difference in dose distribution depending on the type of bowtie filter was visualized by imaging luminance distribution with the PET phantom using a charge-coupled device camera...
February 12, 2018: Radiation Protection Dosimetry
Ahmad Ibrahim Hassan, Martin Skalej, Helmut Schlattl, Christoph Hoeschen
The accuracy of Monte Carlo (MC) simulations in estimating the computed tomography radiation dose is highly dependent on the proprietary x-ray source information. To address this, this study develops a method to precisely estimate the x-ray spectrum and bowtie (BT) filter thickness of the x-ray source based on physical measurements and calculations. The static x-ray source of the CT localizer radiograph was assessed to measure the total filtration at the isocenter for the x-ray spectrum characterization and the BT profile (air-kerma values as a function of fan angle)...
January 2018: Journal of Medical Imaging
Boxuan Shen, Veikko Linko, Kosti Tapio, Siim Pikker, Tibebe Lemma, Ashwin Gopinath, Kurt V Gothelf, Mauri A Kostiainen, J Jussi Toppari
Programmable self-assembly of nucleic acids enables the fabrication of custom, precise objects with nanoscale dimensions. These structures can be further harnessed as templates to build novel materials such as metallic nanostructures, which are widely used and explored because of their unique optical properties and their potency to serve as components of novel metamaterials. However, approaches to transfer the spatial information of DNA constructions to metal nanostructures remain a challenge. We report a DNA-assisted lithography (DALI) method that combines the structural versatility of DNA origami with conventional lithography techniques to create discrete, well-defined, and entirely metallic nanostructures with designed plasmonic properties...
February 2018: Science Advances
George S Krasnov, Nataliya V Melnikova, Valentina A Lakunina, Anastasiya V Snezhkina, Anna V Kudryavtseva, Alexey A Dmitriev
We present MethyMer, a Python-based tool aimed at selecting primers for amplification of complete CpG islands. These regions are difficult in terms of selecting appropriate primers because of their low-complexity, high GC content. Moreover, bisulfite treatment, in fact, leads to the reduction of the 4-letter alphabet (ATGC) to 3-letter one (ATG, except for methylated cytosines), and this also reduces region complexity and increases mispriming potential. MethyMer has a flexible scoring system, which optimizes the balance between various characteristics such as nucleotide composition, thermodynamic features (melting temperature, dimers [Formula: see text]G, etc...
January 30, 2018: Journal of Bioinformatics and Computational Biology
Pengfei Zhan, Te Wen, Zhen-Gang Wang, Yingbo He, Jia Shi, Ting Wang, Xinfeng Liu, Guowei Lu, Baoquan Ding
Metallic bowtie nanoarchitecture can produce dramatic electric field enhancement which is advantageous in single molecule analysis and optical information processing. In the present study, we successfully constructed plasmonic bowtie nanostructures using a DNA origami-based bottom-up assembly strategy, which enables precise control over the geometrical configuration of the bowtie with an approximate 5 nm gap. We accurately positioned a single Raman probe at the gap of the bowtie. Single molecule surface-enhanced Raman scattering (SM-SERS) of individual nanostructures, including ones containing an alkyne group, was observed...
January 27, 2018: Angewandte Chemie
Claire Deeb, Zhi Guo, Ankun Yang, Libai Huang, Teri W Odom
Excited-state interactions between nanoscale cavities and photoactive molecules are critical in plasmonic nano-lasing although the underlying details are less resolved. This paper reports direct visualization of the energy transfer dynamics between two-dimensional arrays of plasmonic gold bowtie nanocavities and dye molecules. Transient absorption microscopy measurements of single bowties within the array surrounded by gain molecules showed fast excited-state quenching (2.6 ± 1 ps) characteristic of individual nanocavities...
January 25, 2018: Nano Letters
Xu Yang, Fei Liu, Yu Zhang, Lu Wang, Yu-Fu Cheng
BACKGROUND: Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance...
December 29, 2017: BMC Genomics
Raman Sankar, Peramaiyan G, Panneer Muthuselvam Irulandi, Suyang Xu, M Zahid Hasan, Fang-Cheng Chou
We report single crystal growth and transport properties of a Weyl semimetal TaAs. Unsaturated large MR about 22100 % at 2 K and 9 T is observed. From the Hall measurement, carrier concentrations n = 4.608×1024 m-3 and p = 3.099×1024 m-3, and mobilities μp = 2.502 m2 V-1 s-1 and μn = 16.785 m2 V-1 s-1 at 2 K are extracted. The de Haas-van Alphen (dHvA) oscillations at 2 K and 9 T suggest the presence of a Fermi surface, and the quantum electronic parameters such as effective cyclotron mass and Dingle temperature were obtained using Lifshitz-Kosevich (L-K) fitting...
November 14, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Priten B Savaliya, Arun Thomas, Rishi Dua, Anuj Dhawan
We propose the design of switchable plasmonic nanoantennas (SPNs) that can be employed for optical switching in the near-infrared regime. The proposed SPNs consist of nanoantenna structures made up of a plasmonic metal (gold) such that these nanoantennas are filled with a switchable material (vanadium dioxide). We compare the results of these SPNs with inverted SPN structures that consist of gold nanoantenna structures surrounded by a layer of vanadium dioxide (VO2) on their outer surface. These nanoantennas demonstrate switching of electric-field intensity enhancement (EFIE) between two states (On and Off states), which can be induced thermally, optically or electrically...
October 2, 2017: Optics Express
Punnag Padhy, Mohammad Asif Zaman, Paul Hansen, Lambertus Hesselink
Nanoparticles trapped on resonant near-field apertures/engravings carved in plasmonic films experience optical forces due to the steep intensity gradient field of the aperture/engraving as well as the image like interaction with the substrate. For non-resonant nanoparticles the contribution of the substrate interaction to the trapping force in the vicinity of the trap (aperture/engraving) mode is negligible. But, in the case of plasmonic nanoparticles, the contribution of the substrate interaction to the low frequency stable trapping mode of the coupled particle-trap system increases as their resonance is tuned to the trap resonance...
October 16, 2017: Optics Express
Chunrui Han, Edward P J Parrott, Georges Humbert, Aurelian Crunteanu, Emma Pickwell-MacPherson
Broadband modulation of terahertz (THz) light is experimentally realized through the electrically driven metal-insulator phase transition of vanadium dioxide (VO2) in hybrid metal antenna-VO2 devices. The devices consist of VO2 active layers and bowtie antenna arrays, such that the electrically driven phase transition can be realized by applying an external voltage between adjacent metal wires extended to a large area array. The modulation depth of the terahertz light can be initially enhanced by the metal wires on top of VO2 and then improved through the addition of specific bowties in between the wires...
October 5, 2017: Scientific Reports
Omran Ahmadi, Seyed Bagher Mortazavi, Ali Khavanin, Hamidreza Mokarami
BACKGROUND: Accident analysis is the main aspect of accident investigation. It includes the method of connecting different causes in a procedural way. Therefore, it is important to use valid and reliable methods for the investigation of different causal factors of accidents, especially the noteworthy ones. OBJECTIVE: This study aimed to prominently assess the accuracy (sensitivity index [SI]) and consistency of the six most commonly used accident analysis methods in the petroleum industry...
November 17, 2017: International Journal of Occupational Safety and Ergonomics: JOSE
Kui-Ying Nie, Jing Li, Xuanhu Chen, Yang Xu, Xuecou Tu, Fang-Fang Ren, Qingguo Du, Lan Fu, Lin Kang, Kun Tang, Shulin Gu, Rong Zhang, Peiheng Wu, Youdou Zheng, Hark Hoe Tan, Chennupati Jagadish, Jiandong Ye
Intermediate band solar cells (IBSCs) are conceptual and promising for next generation high efficiency photovoltaic devices, whereas, IB impact on the cell performance is still marginal due to the weak absorption of IB states. Here a rational design of a hybrid structure composed of ZnTe:O/ZnO core-shell nanowires (NWs) with Al bowtie nanoantennas is demonstrated to exhibit strong ability in tuning and enhancing broadband light response. The optimized nanowire dimensions enable absorption enhancement by engineering leaky-mode dielectric resonances...
August 8, 2017: Scientific Reports
Bin Tian, Shichen Wang, Timothy C Todd, Charles D Johnson, Guiliang Tang, Harold N Trick
BACKGROUND: The soybean cyst nematode (SCN), Heterodera glycines, is one of the most devastating diseases limiting soybean production worldwide. It is known that small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play important roles in regulating plant growth and development, defense against pathogens, and responses to environmental changes. RESULTS: In order to understand the role of soybean miRNAs during SCN infection, we analyzed 24 small RNA libraries including three biological replicates from two soybean cultivars (SCN susceptible KS4607, and SCN HG Type 7 resistant KS4313N) that were grown under SCN-infested and -noninfested soil at two different time points (SCN feeding establishment and egg production)...
August 2, 2017: BMC Genomics
Wenhua Jiang, Pengfei Liu, Xiaodong Li
Breast cancer (BC) is the most common type of malignancy in females worldwide, however, its underlying mechanisms remain poorly understood. The present study aimed to investigate the mechanisms behind the development and progression of BC and identify potential biomarkers for it. The chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) dataset GSM1642516 and gene expression dataset GSE34925 were downloaded from the Gene Expression Omnibus database. Affy and oligo packages were used for the background correction and normalization of the gene expression dataset...
June 2017: Oncology Letters
Latha Battu, Mettu Madhavi Reddy, Burragoni Sravanthi Goud, Kayalvili Ulaganathan, Kandasamy Ulaganathan
Reference based assembly of genomic reads of the elite indica rice cultivar RP Bio-226 was carried out against 2101 reference bacterial genomes using Bowtie-2 genome assembly tool. Five types of data: Number of paired end reads concordantly aligned exactly only once, number of paired end reads concordantly aligned more than once, number of mates that make the pairs aligned exactly only once, number of mates that make the pairs aligned more than once and overall percentage of alignment were collected. Interpretation of the results and identification of endophytes based on these alignment statistics are described in detail in our research article "L...
June 2017: Data in Brief
Wenzhao Sun, Bin Wang, Bo Qiu, Jian Liang, Weihao Xie, Xiaowu Deng, Zhenyu Qi
OBJECTIVE: To assess the breast dose during a routine thoracic cone-beam CT (CBCT) check with the efforts to explore the possible dose reduction strategy. MATERIALS AND METHODS: Metal oxide semiconductor field-effect transistor (MOSFET) dosimeters were used to measure breast surface doses during a thorax kV CBCT scan in an anthropomorphic phantom. Breast doses for different scanning protocols and breast sizes were compared. Dose reduction was attempted by using partial arc CBCT scan with bowtie filter...
March 21, 2017: Oncotarget
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