Read by QxMD icon Read


Dapeng Wang
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for an easy-to-learn workflow to cope with the increased demands from a large number of laboratories across the world. We report a one-in-all solution called hppRNA, composed of four scenarios such as pre-mapping, core-workflow, post-mapping and sequence variation detection, written by a series of individual Perl and R scripts, counting on well-established and preinstalled software, irrespective of single-end or paired-end, unstranded or stranded sequencing method...
January 17, 2017: Briefings in Bioinformatics
Ho Lee, Benjamin Fahimian, Lei Xing
This paper proposes a binary moving-blocker (BMB)-based technique for scatter correction in cone-beam computed tomography (CBCT). In concept, a beam blocker consisting of lead strips, mounted in front of the x-ray tube, moves rapidly in and out of the beam during a single gantry rotation. The projections are acquired in alternating phases of blocked and unblocked cone beams, where the blocked phase results in a stripe pattern in the width direction. To derive the scatter map from the blocked projections, one-dimensional B-Spline interpolation/extrapolation is applied by using the detected information in the shaded regions...
January 12, 2017: Physics in Medicine and Biology
R Kramer, V F Cassola, M E A Andrade, M W C de Araújo, D J Brenner, H J Khoury
The purpose of bowtie filters in CT scanners is to homogenize the x-ray intensity measured by the detectors in order to improve the image quality and at the same time to reduce the dose to the patient because of the preferential filtering near the periphery of the fan beam. For CT dosimetry, especially for Monte Carlo calculations of organ and tissue absorbed doses to patients, it is important to take the effect of bowtie filters into account. However, material composition and dimensions of these filters are proprietary...
February 7, 2017: Physics in Medicine and Biology
I Ali, S Hossain, E Syzek, S Ahmad
PURPOSE: To quantitatively investigate the surface dose deposited in patients imaged with a kV on-board-imager mounted on a radiotherapy machine using different clinical imaging techniques and filters. METHODS: A high sensitivity photon diode is used to measure the surface dose on central-axis and at an off-axis-point which is mounted on the top of a phantom setup. The dose is measured for different imaging techniques that include: AP-Pelvis, AP-Head, AP-Abdomen, AP-Thorax, and Extremity...
June 2016: Medical Physics
C Hua, W Yao, T Kidani, J Farr, K Tomida, S Ozawa, T Nishimura, T Fujusawa, R Shinagawa, T Merchant
PURPOSE: To describe the design and performance of a ceiling-mounted robotic C-arm CBCT system for image-guided proton therapy. METHODS: Uniquely different from traditional C-arm CBCT used in interventional radiology, the imaging system was designed to provide volumetric image guidance for patients treated on a 190-degree proton gantry system and a 6 degree-of-freedom (DOF) robotic patient positioner. The mounting of robotic arms to the ceiling rails, rather than gantry or nozzle, provides the flexibility in imaging locations (isocenter, iso+27cm in X, iso+100cm in Y) in the room and easier upgrade as technology advances...
June 2016: Medical Physics
J Hoffman, F Noo, S Young, M McNitt-Gray
PURPOSE: Recent work has shown that current TCM profile designs boost detection of low-contrast lung lesions in the lung apices, but yield reduced detection performance in the mid and lower lung regions relative to fixed tube current cases. This observed imbalance suggests that the TCM scheme might be tailored in new ways to maximize nodule detection throughout the entire lung. In this work, we begin a preliminary investigation into custom TCM profiles in an attempt to achieve uniform lesion detection throughout the extent of the lung...
June 2016: Medical Physics
T Liu, H Lin, Y Gao, P Caracappa, G Wang, W Cong, X Xu
PURPOSE: Dynamic bowtie filter is an innovative design capable of modulating the X-ray and balancing the flux in the detectors, and it introduces a new way of patient-specific CT scan optimizations. This study demonstrates the feasibility of performing fast Monte Carlo dose calculation for a type of dynamic bowtie filter for cone-beam CT (Liu et al. 2014 9(7) PloS one) using MIC coprocessors. METHODS: The dynamic bowtie filter in question consists of a highly attenuating bowtie component (HB) and a weakly attenuating bowtie (WB)...
June 2016: Medical Physics
S Kim, D Rangaraj
PURPOSE: Although cone-beam CT (CBCT) imaging became popular in radiation oncology, its imaging dose estimation is still challenging. The goal of this study is to assess the kilovoltage CBCT doses using GMctdospp - an EGSnrc based Monte Carlo (MC) framework. METHODS: Two Varian OBI x-ray tube models were implemented in the GMctpdospp framework of EGSnrc MC System. The x-ray spectrum of 125 kVp CBCT beam was acquired from an EGSnrc/BEAMnrc simulation and validated with IPEM report 78...
June 2016: Medical Physics
H Youn, J Kim, H Jeon, H Kim, M Cho, S Yun, J Nam, J Lee, J Lee, D Park, W Kim, Y Ki, D Kim
PURPOSE: To investigate the feasibility of an analytic framework to estimate patients' absorbed dose distribution owing to daily cone-beam CT scan for image-guided radiation treatment. METHODS: To compute total absorbed dose distribution, we separated the framework into primary and scattered dose calculations. Using the source parameters such as voltage, current, and bowtie filtration, for the primary dose calculation, we simulated the forward projection from the source to each voxel of an imaging object including some inhomogeneous inserts...
June 2016: Medical Physics
J Xu, A Sisniega, W Zbijewski, H Dang, J Stayman, X Wang, D Foos, N Aygun, V Koliatsos, J Siewerdsen
PURPOSE: This work reports the design, development, and first technical assessment of a cone-beam CT (CBCT) scanner developed specifically for imaging of acute intracranial hemorrhage (ICH) at the point of care, with target applications in diagnosis and monitoring of traumatic brain injury, stroke, and postsurgical hemorrhage. METHODS: System design employed a task-based image quality model to quantify the influence of factors such as additive noise and high-gain (HG) detector readout on ICH detectability...
June 2016: Medical Physics
Yifang Zhou, Jessica Nute, Alexander Scott, Christina Lee
PURPOSE: For CT dose optimization, one needs to address two important questions. The first is how various lesion specific detection tasks demand different patient doses for the same patient. The second is how the variation of the patient size requires different patient doses for the same lesion detection task. In this study, we attempted to find quantitative solutions to these questions by utilizing a wide range of abdomen phantoms. METHODS: A simplified model with a monochromatic fan-beam passing through a bowtie filter and an elliptical object was proposed...
December 31, 2016: Medical Physics
Yang Chen, Jin Qin, Jianfeng Chen, Liang Zhang, Chengfu Ma, Jiaru Chu, Xianfan Xu, Liang Wang
Photolithography has long been a critical technology for nanoscale manufacturing, especially in the semiconductor industry. However, the diffractive nature of light has limited the continuous advance of optical lithography resolution. To overcome this obstacle, near-field scanning optical lithography (NSOL) is an alternative low-cost technique, whose resolution is determined by the near-field localization that can be achieved. Here, we apply the newly-developed backside milling method to fabricate bowtie apertures with a sub-15 nm gap, which can substantially improve the resolution of NSOL...
February 3, 2017: Nanotechnology
A A Lyamkina, K Schraml, A Regler, M Schalk, A K Bakarov, A I Toropov, S P Moshchenko, Michael Kaniber
Deterministically integrating semiconductor quantum emitters with plasmonic nano-devices paves the way towards chip-scale integrable, true nanoscale quantum photonic technologies. For this purpose, stable and bright semiconductor emitters are needed, which moreover allow for CMOS-compatibility and optical activity in the telecommunication band. Here, we demonstrate strongly enhanced light-matter coupling of single near-surface (< 10 nm) InAs quantum dots monolithically integrated into electromagnetic hot-spots of sub-wavelength sized metal nanoantennas...
December 12, 2016: Optics Express
Lin Peng, Ji-Yang Xie, Kai Sun, Xing Jiang, Si-Min Li
In this research, the novel concept of a resonance-based reflector (RBR) was proposed, and a ring-shaped RBR was utilized to design a unidirectional antenna with low-profile and broadband characteristics. Research found the ring operates as two half-wavelength (λ/2) resonators. Then, the resonance effect transforms the reflection phase of the ring RBR, and achieves a reflection phase of 0° < ϕ < 180° in a wide frequency range above the resonance. Then, the in-phase reflection characteristic (-90° < ϕ < 90°) can be obtained in the wide frequency band by placing an antenna above the RBR with a distance smaller than λ/4...
December 9, 2016: Sensors
Dezso Modos, Johanne Brooks, David Fazekas, Eszter Ari, Tibor Vellai, Peter Csermely, Tamas Korcsmaros, Katalin Lenti
Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in human signaling networks, we developed a signaling network-based method using cross-talk annotation and tissue-specific signaling flow analysis. 75 CPGs were found with higher degree, betweenness centrality, closeness, and 'bowtieness' when compared to other paralogs or other proteins in the signaling network...
December 6, 2016: Scientific Reports
Boyeol Yoo, Kihong Son, Rizza Pua, Jinsung Kim, Alexander Solodov, Seungryong Cho
OBJECTIVES: With the increased use of computed tomography (CT) in clinics, dose reduction is the most important feature people seek when considering new CT techniques or applications. We developed an intensity-weighted region-of-interest (IWROI) imaging method in an exact half-fan geometry to reduce the imaging radiation dose to patients in cone-beam CT (CBCT) for image-guided radiation therapy (IGRT). While dose reduction is highly desirable, preserving the high-quality images of the ROI is also important for target localization in IGRT...
October 2016: Healthcare Informatics Research
Ute Christine Ehlers, Eirin Olaussen Ryeng, Edward McCormack, Faisal Khan, Sören Ehlers
The safety effects of cooperative intelligent transport systems (C-ITS) are mostly unknown and associated with uncertainties, because these systems represent emerging technology. This study proposes a bowtie analysis as a conceptual framework for evaluating the safety effect of cooperative intelligent transport systems. These seek to prevent road traffic accidents or mitigate their consequences. Under the assumption of the potential occurrence of a particular single vehicle accident, three case studies demonstrate the application of the bowtie analysis approach in road traffic safety...
November 25, 2016: Accident; Analysis and Prevention
Christos Boutopoulos, Adrien Dagallier, Maria Sansone, Andre-Pierre Blanchard-Dionne, Évelyne Lecavalier-Hurtubise, Étienne Boulais, Michel Meunier
Precise spatial and temporal control of pressure stimulation at the nanometer scale is essential for the fabrication and manipulation of nano-objects, and for exploring single-molecule behaviour of matter under extreme conditions. However, state-of-the-art nano-mechanical transducers require sophisticated driving hardware and are currently limited to moderate pressure regimes. Here we report a gold plasmonic bowtie (AuBT) nano-antennas array that can generate extreme pressure stimulus of ∼100 GPa in the ps (10(-12) s) time scale with sub-wavelength resolution upon irradiation with ultra-short laser pulses...
October 6, 2016: Nanoscale
Dete van Eeden, Freek du Plessis
INTRODUCTION: A mathematical 3D model of an existing computed tomography (CT) scanner was created and used in the EGSnrc-based BEAMnrc and egs_cbct Monte Carlo codes. Simulated transmission dose profiles of a RMI-465 phantom were analysed to verify Hounsfield numbers against measured data obtained from the CT scanner. METHODS AND MATERIALS: The modelled CT unit is based on the design of a Toshiba Aquilion 16 LB CT scanner. As a first step, BEAMnrc simulated the X-ray tube, filters, and secondary collimation to obtain phase space data of the X-ray beam...
October 2016: Physica Medica: PM
Yu Lu, Guangqing Du, Feng Chen, Qing Yang, Hao Bian, Jiale Yong, Xun Hou
In this paper, the tunable optical trapping dependence on wavelength of incident beam is theoretically investigated based on numerical simulations. The Monte Carlo method is taken into account for exploring the trapping characteristics such as average deviation and number distribution histogram of nanoparticles. It is revealed that both the width and the depth of potential well for trapping particles can be flexibly adjusted by tuning the wavelength of the incident beam. In addition, incident wavelengths for the deepest potential well and for the strongest stiffness at bottom are separated...
September 26, 2016: Scientific Reports
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"