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Judd F Hultquist, Kathrin Schumann, Jonathan M Woo, Lara Manganaro, Michael J McGregor, Jennifer Doudna, Viviana Simon, Nevan J Krogan, Alexander Marson
New genetic tools are needed to understand the functional interactions between HIV and human host factors in primary cells. We recently developed a method to edit the genome of primary CD4(+) T cells by electroporation of CRISPR/Cas9 ribonucleoproteins (RNPs). Here, we adapted this methodology to a high-throughput platform for the efficient, arrayed editing of candidate host factors. CXCR4 or CCR5 knockout cells generated with this method are resistant to HIV infection in a tropism-dependent manner, whereas knockout of LEDGF or TNPO3 results in a tropism-independent reduction in infection...
October 25, 2016: Cell Reports
Georgios N Panagopoulos, Panayiotis D Megaloikonomos, Andreas F Mavrogenis
Peripheral nerve injury can have a potentially devastating impact on a patient's quality of life, resulting in severe disability with substantial social and personal cost. Refined microsurgical techniques, advances in peripheral nerve topography, and a better understanding of the pathophysiology and molecular basis of nerve injury have all led to a decisive leap forward in the field of translational neurophysiology. Nerve repair, nerve grafting, and nerve transfers have improved significantly with consistently better functional outcomes...
October 25, 2016: Orthopedics
Aaron C W Lin, Wendy Strugnell, Robyn Riley, Benjamin Schmitt, Michael Zenge, Michaela Schmidt, Norman R Morris, Christian Hamilton-Craig
PURPOSE: To assess the clinical feasibility of a compressed sensing cine magnetic resonance imaging (MRI) sequence of both high temporal and spatial resolution (CS_bSSFP) in comparison to a balanced steady-state free precession cine (bSSFP) sequence for reliable quantification of left ventricular (LV) volumes and mass. MATERIALS AND METHODS: Segmented MRI cine images were acquired on a 1.5T scanner in 50 patients in the LV short-axis stack orientation using a retrospectively gated conventional bSSFP sequence (generalized autocalibrating partially parallel acquisition [GRAPPA] acceleration factor 2), followed by a prospectively triggered CS_bSSFP sequence with net acceleration factor of 8...
October 26, 2016: Journal of Magnetic Resonance Imaging: JMRI
Yu P Semochkina, E Yu Moskaleva
Stem cell cultures are heterogeneous and include true stem cells and progenitor cells. True stem cells are identified by flow cytofluorometry as a cell subset characterized by low accumulation of fluorescent dye rhodamin-123 and forming a side population. Low-dose γ-irradiation (10-200 mGy) of human skin epithelial stem cells and epithelial H69 tumor cells to was followed by an increase in cell counts by day 7 after the exposure. In parallel, reduction of the side population to 4-30% from the control for epithelial stem cells on the next day after exposure and to 22-36% from the control for H69 cells in 3 days after exposure...
October 26, 2016: Bulletin of Experimental Biology and Medicine
Masaaki Nakayama, Yoshindo Kawaguchi, Takashi Akiba, Masao Kim, Hidemune Naito, Shigeko Hara, Teruhiko Maeba, Noriaki Yorioka, James A Sloand, Mark R Marshall
BACKGROUND: We report here two new peritoneal dialysis fluids (PDFs) for Japan [BLR 250, BLR 350 (Baxter Limited, Japan)]. The PDFs use two-chamber systems, and have bicarbonate and lactate buffer to a total of 35 mmol/L. In separate trials, the new PDFs were compared to two "standard" systems [PD-4, PD-2 (Baxter Limited, Japan)]. The trials aimed to demonstrate non-inferiority of peritoneal creatinine clearance (pCcr), peritoneal urea clearance (pCurea) and ultrafiltration volume (UF), and compare acid-base and electrolyte balance...
October 25, 2016: Clinical and Experimental Nephrology
Bartosz Kazimierz Słowikowski, Margarita Lianeri, Paweł Piotr Jagodziński
It is well known that a connection between xenobiotics inhalation, especially tobacco combustion and Lung Cancer development is strongly significant and indisputable. However, recent studies provide evidence indicating that another factors such as, estrogens are also involved in lung carcinoma biology and metabolism. Although the status of estrogen receptors (ER), in both cancerous and healthy lung tissue has been well documented, there is still inconclusive data with respect of which isoform of the receptor is present in the lungs...
October 25, 2016: Molecular Biology Reports
Wenbing Wang, Yanqing Wu
1,1,1-Trichloroethane (1,1,1-TCA), a dense non-aqueous phase liquid (DNAPL), is relatively slow to remediate naturally; combination of zero-valent iron and immobilized microorganism is a potential means to accelerate DNAPL biodegradation. We first adopted high density luffa sponge (HDLS) as immobilized microorganism carrier. The experimental results demonstrated that (1) the supernatant liquid microorganisms were the optimal immobilized microorganisms for HDLS and (2) the combination of zero-valent iron and immobilized microorganisms accelerated 1,1,1-TCA transformation...
October 25, 2016: Applied Microbiology and Biotechnology
Colin Echeverría Aitken, Petra Beznosková, Vladislava Vlčkova, Wen-Ling Chiu, Fujun Zhou, Leoš Shivaya Valášek, Alan G Hinnebusch, Jon R Lorsch
Eukaryotic translation initiation factor 3 (eIF3) is a central player in recruitment of the pre-initiation complex (PIC) to mRNA. We probed the effects on mRNA recruitment of a library of S. cerevisiae eIF3 functional variants spanning its 5 essential subunits using an in vitro-reconstituted system. Mutations throughout eIF3 disrupt its interaction with the PIC and diminish its ability to accelerate recruitment to a native yeast mRNA. Alterations to the eIF3a CTD and eIF3b/i/g significantly slow mRNA recruitment, and mutations within eIF3b/i/g destabilize eIF2•GTP•Met-tRNAi binding to the PIC...
October 26, 2016: ELife
Anna Torres, Joanna Kozak, Agnieszka Korolczuk, Paulina Wdowiak, Ewa Domańska-Glonek, Ryszard Maciejewski, Kamil Torres
BACKGROUND: Endometrial cancer is the most common cancer of the female reproductive tract. Based on our previous studies we speculated that miR-92a exhibited pro-oncogenic properties in endometrial cancer, and therefore its inhibition could be used as a therapeutic measure in this disease. Therefore in the present study we aimed to investigate both in vitro and in vivo if inhibition of miR-92a in endometrial cancer would limit cancer cells proliferation. METHODS: miR-92a expression was evaluated in four endometrial cancer cell lines using qPCR...
October 26, 2016: BMC Cancer
Austin M Faught, Michael Trager, Fang-Fang Yin, John Kirkpatrick, Justus Adamson
PURPOSE: The recent development of multifocal stereotactic radiosurgery (SRS) using a single isocenter volumetric modulated arc theory (VMAT) technique warrants a re-examination of the quality assurance (QA) tolerances for routine mechanical QA recommended by the American Association of Physicists in Medicine Task Group Report Number 142. Multifocal SRS can result in targets with small volumes being at a large off-axis distance from the treatment isocenter. Consequently, angular errors in the collimator, patient support assembly (PSA), or gantry could have an increased impact on target coverage...
October 2016: Medical Physics
Morgan C Lyon, Arkadiusz Sitek, Scott D Metzler, Stephen C Moore
PURPOSE: The authors are currently developing a dual-resolution multiple-pinhole microSPECT imaging system based on three large NaI(Tl) gamma cameras. Two multiple-pinhole tungsten collimator tubes will be used sequentially for whole-body "scout" imaging of a mouse, followed by high-resolution (hi-res) imaging of an organ of interest, such as the heart or brain. Ideally, the whole-body image will be reconstructed in real time such that data need only be acquired until the area of interest can be visualized well-enough to determine positioning for the hi-res scan...
October 2016: Medical Physics
Seyoun Park, Todd McNutt, William Plishker, Harry Quon, John Wong, Raj Shekhar, Junghoon Lee
PURPOSE: Accurate tracking of anatomical changes and computation of actually delivered dose to the patient are critical for successful adaptive radiation therapy (ART). Additionally, efficient data management and fast processing are practically important for the adoption in clinic as ART involves a large amount of image and treatment data. The purpose of this study was to develop an accurate and efficient Software platform for CUmulative Dose Assessment (scuda) that can be seamlessly integrated into the clinical workflow...
October 2016: Medical Physics
Svenja Ipsen, Ralf Bruder, Rick O'Brien, Paul J Keall, Achim Schweikard, Per R Poulsen
PURPOSE: With the trend in radiotherapy moving toward dose escalation and hypofractionation, the need for highly accurate targeting increases. While MLC tracking is already being successfully used for motion compensation of moving targets in the prostate, current real-time target localization methods rely on repeated x-ray imaging and implanted fiducial markers or electromagnetic transponders rather than direct target visualization. In contrast, ultrasound imaging can yield volumetric data in real-time (3D + time = 4D) without ionizing radiation...
October 2016: Medical Physics
Naomi Nitschke, Kalina Atkovska, Jochen S Hub
Molecular dynamics simulations are capable of predicting the permeability of lipid membranes for drug-like solutes, but the calculations have remained prohibitively expensive for high-throughput studies. Here, we analyze simple measures for accelerating potential of mean force (PMF) calculations of membrane permeation, namely, (i) using smaller simulation systems, (ii) simulating multiple solutes per system, and (iii) using shorter cutoffs for the Lennard-Jones interactions. We find that PMFs for membrane permeation are remarkably robust against alterations of such parameters, suggesting that accurate PMF calculations are possible at strongly reduced computational cost...
September 28, 2016: Journal of Chemical Physics
A E Dyson, C Thornton, S M Hooker
We describe in detail a low power Compact Marx Bank (CMB) circuit that can provide 20 kV, 500 A pulses of approximately 100-200 ns duration. One application is the generation of capillary discharge plasmas of density ≈10(18) cm(-3) used in laser plasma accelerators. The CMB is triggered with a high speed solid state switch and gives a high voltage output pulse with a ns scale rise time into a 50 Ω load (coaxial cable) with <4 ns voltage jitter. Its small size (10 cm  ×  25 cm  ×  5 cm) means that it can be placed right next to the capillary discharge in the target chamber to avoid the need to impedance match...
September 2016: Review of Scientific Instruments
Wei-Huang Wu, Yuan Tian, Jie Luo, Cheng-Gang Shao, Jia-Hao Xu, Dian-Hong Wang
In the measurement of the gravitational constant G with angular acceleration method, the accurate estimation of the amplitude of the useful angular acceleration generated by source masses depends on the effective subtraction of the spurious gravitational signal caused by room fixed background masses. The gravitational background signal is of time-varying frequency, and mainly consists of the prominent fundamental frequency and second harmonic components. We propose an improved correlation method to estimate the amplitudes of the prominent components of the gravitational background signal with high precision...
September 2016: Review of Scientific Instruments
Zhengyong Duan, Chuansheng Tang, Yang Li, Junliang Han, Guoxiong Wu
Pulse shaping techniques are discussed in this paper for the practicability of a developed high-g shock tester. The tester is based on collision principle where there is a one-level velocity amplifier. A theoretical and experimental study of pulse shaping techniques is presented. A model was built and theoretical formulae were deduced for the shock peak acceleration and its duration. Then theoretical analysis and some experiments were conducted. The test results verify the validity of theoretical model and show that the shock tester can generate the expected high-g shock pulses by integrated usage of different impact velocities and pulse shapers made from different materials...
September 2016: Review of Scientific Instruments
T Xin, J C Brutus, Sergey A Belomestnykh, I Ben-Zvi, C H Boulware, T L Grimm, T Hayes, Vladimir N Litvinenko, K Mernick, G Narayan, P Orfin, I Pinayev, T Rao, F Severino, J Skaritka, K Smith, R Than, J Tuozzolo, E Wang, B Xiao, H Xie, A Zaltsman
High-bunch-charge photoemission electron-sources operating in a continuous wave (CW) mode are required for many advanced applications of particle accelerators, such as electron coolers for hadron beams, electron-ion colliders, and free-electron lasers. Superconducting RF (SRF) has several advantages over other electron-gun technologies in CW mode as it offers higher acceleration rate and potentially can generate higher bunch charges and average beam currents. A 112 MHz SRF electron photoinjector (gun) was developed at Brookhaven National Laboratory to produce high-brightness and high-bunch-charge bunches for the coherent electron cooling proof-of-principle experiment...
September 2016: Review of Scientific Instruments
S F Carr, R Garnett, C S Lo
Controlling molecule-surface interactions is key for chemical applications ranging from catalysis to gas sensing. We present a framework for accelerating the search for the global minimum on potential surfaces, corresponding to stable adsorbate-surface structures. We present a technique using Bayesian inference that enables us to predict converged density functional theory potential energies with fewer self-consistent field iterations. We then discuss how this technique fits in with the Bayesian Active Site Calculator, which applies Bayesian optimization to the problem...
October 21, 2016: Journal of Chemical Physics
Ruiliang Bai, Dan Benjamini, Jian Cheng, Peter J Basser
Previously, we showed that compressive or compressed sensing (CS) can be used to reduce significantly the data required to obtain 2D-NMR relaxation and diffusion spectra when they are sparse or well localized. In some cases, an order of magnitude fewer uniformly sampled data were required to reconstruct 2D-MR spectra of comparable quality. Nonetheless, this acceleration may still not be sufficient to make 2D-MR spectroscopy practicable for many important applications, such as studying time-varying exchange processes in swelling gels or drying paints, in living tissue in response to various biological or biochemical challenges, and particularly for in vivo MRI applications...
October 21, 2016: Journal of Chemical Physics
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