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https://www.readbyqxmd.com/read/28437939/exploiting-high-order-phase-shift-keying-modulation-and-direct-detection-in-silicon-photonic-systems
#1
Jie You, Nicolae C Panoiu
A computational approach to evaluate the bit-error ratio (BER) in silicon photonic systems employing high-order phase-shift keying (PSK) modulation formats is presented. Specifically, the investigated systems contain a silicon based optical interconnect, namely a strip silicon photonic waveguide or a silicon photonic crystal waveguide, and direct-detection receivers suitable to detect PSK and amplitude-shaped PSK signals. The superposition of a PSK signal and complex additive white Gaussian noise passes through the optical interconnect and subsequently through two detection-branch receivers...
April 17, 2017: Optics Express
https://www.readbyqxmd.com/read/28437900/model-and-reconstruction-of-a-k-edge-contrast-agent-distribution-with-an-x-ray-photon-counting-detector
#2
Bo Meng, Wenxiang Cong, Yan Xi, Bruno De Man, Jian Yang, Ge Wang
Contrast-enhanced computed tomography (CECT) helps enhance the visibility for tumor imaging. When a high-Z contrast agent interacts with X-rays across its K-edge, X-ray photoelectric absorption would experience a sudden increment, resulting in a significant difference of the X-ray transmission intensity between the left and right energy windows of the K-edge. Using photon-counting detectors, the X-ray intensity data in the left and right windows of the K-edge can be measured simultaneously. The differential information of the two kinds of intensity data reflects the contrast-agent concentration distribution...
April 17, 2017: Optics Express
https://www.readbyqxmd.com/read/28437735/detective-quantum-efficiency-dqe-in-pet-scanners-a-simulation-study
#3
George E Karpetas, Christos M Michail, George P Fountos, Nektarios I Kalyvas, Ioannis G Valais, Ioannis S Kandarakis, George S Panayiotakis
The aim of the present study is to introduce the detective quantum efficiency (DQE) for the image quality assessment of positron emission tomography (PET) scanners. For this purpose, a thin layer chromatography (TLC) plane source was simulated using a previously validated, scanner and source geometry, Monte Carlo (MC) model. The model was developed with the Geant4 application for tomographic emission (GATE) MC package and reconstructed images obtained with the software for tomographic image reconstruction (STIR), with cluster computing...
April 12, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28437676/superior-inferior-position-of-patellar-component-affects-patellofemoral-kinematics-and-contact-forces-in-computer-simulation
#4
Shinichiro Nakamura, Yoshihisa Tanaka, Shinichi Kuriyama, Kohei Nishitani, Hiromu Ito, Moritoshi Furu, Shuichi Matsuda
BACKGROUND: Anterior knee pain has been reported as a major postoperative complication after total knee arthroplasty, which may lead to patient dissatisfaction. Rotational alignment and the medial-lateral position correlate with patellar maltracking, which can cause knee pain postoperatively. However, the superior-inferior position of the patellar component has not been investigated. The purpose of the current study was to investigate the effects of the patellar superior-inferior position on patellofemoral kinematics and kinetics...
April 18, 2017: Clinical Biomechanics
https://www.readbyqxmd.com/read/28437618/state-of-the-art-calculations-of-sublimation-enthalpies-for-selected-molecular-crystals-and-their-computational-uncertainty
#5
Ctirad Červinka, Michal Fulem
A computational methodology for calculation of sublimation enthalpies of molecular crystals from first principles is developed and validated by comparison to critically evaluated literature experimental data. Temperature dependent sublimation enthalpies for a set of selected 22 molecular crystals in their low-temperature phases are calculated. The computational methodology consists in several building blocks based on high level electronic structure methods of quantum chemistry and statistical thermodynamics...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437561/semiparametric-probit-models-with-univariate-and-bivariate-current-status-data
#6
Hao Liu, Jing Qin
Multivariate current-status data are frequently encountered in biomedical and public health studies. Semiparametric regression models have been extensively studied for univariate current-status data, but most existing estimation procedures are computationally intensive, involving either penalization or smoothing techniques. It becomes more challenging for the analysis of multivariate current-status data. In this article, we study the maximum likelihood estimations for univariate and bivariate current-status data under the semiparametric probit regression models...
April 24, 2017: Biometrics
https://www.readbyqxmd.com/read/28437460/an-aggregation-removal-model-for-the-formation-and-size-determination-of-post-synaptic-scaffold-domains
#7
Jonas Ranft, Leandro G Almeida, Pamela C Rodriguez, Antoine Triller, Vincent Hakim
The formation and stability of synapses are key questions in neuroscience. Post-synaptic domains have been classically conceived as resulting from local insertion and turnover of proteins at the synapse. However, insertion is likely to occur outside the post-synaptic domains and advances in single-molecule imaging have shown that proteins diffuse in the plane of the membrane prior to their accumulation at synapses. We quantitatively investigated this scenario using computer simulations and mathematical analysis, taking for definiteness the specific case of inhibitory synapse components, i...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28437426/representational-models-a-common-framework-for-understanding-encoding-pattern-component-and-representational-similarity-analysis
#8
Jörn Diedrichsen, Nikolaus Kriegeskorte
Representational models specify how activity patterns in populations of neurons (or, more generally, in multivariate brain-activity measurements) relate to sensory stimuli, motor responses, or cognitive processes. In an experimental context, representational models can be defined as hypotheses about the distribution of activity profiles across experimental conditions. Currently, three different methods are being used to test such hypotheses: encoding analysis, pattern component modeling (PCM), and representational similarity analysis (RSA)...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28437362/sonotubometric-assessment-for-severity-of-patulous-eustachian-tube
#9
Iori Takata, Ryoukichi Ikeda, Tetsuaki Kawase, Yoko Suzuki, Takeshi Sato, Yukio Katori, Toshimitsu Kobayashi
OBJECTIVE: To investigate the relationship between the morphological patency of the eustachian tube (ET) and sound transmission via the ET. STUDY DESIGN: Retrospective chart review and model experiment. SETTING: Tertiary referral center. SUBJECTS: A total of 56 ears of 28 patients (9 men and 19 women, aged from 12 to 82 yr, mean 40.4 ± 21.5 yr) who underwent sonotubometric measurement using postural change as well as computed tomography (CT) of the ET in the sitting position, including 26 ears with definite patulous ET, 9 ears with possible patulous ET, and 21 ears without patulous ET...
April 21, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28437349/a-new-navigational-tool-for-pedicle-screw-placement-in-patients-with-severe-scoliosis-a-pilot-study-to-prove-feasibility-accuracy-and-identify-operative-challenges
#10
Michael Putzier, Patrick Strube, Riccardo Cecchinato, Claudio Lamartina, Eike K Hoff
STUDY DESIGN: Pilot study. OBJECTIVE: To develop and validate the feasibility and accuracy of a newly designed navigational spinal instrument guiding tool for patient-matched thoracic and lumbar pedicle screw placement in patients with severe scoliosis, and to identify intraoperative challenges that may be relevant. SUMMARY OF BACKGROUND DATA: Pedicle screw placement is challenging in severely rotated scoliotic spine with small diameters and asymmetrical shape of the pedicles and vertebrae...
May 2017: Clinical Spine Surgery
https://www.readbyqxmd.com/read/28437193/evaluation-of-the-effects-of-photobiomodulation-on-biomechanical-properties-and-hounsfield-unit-of-partial-osteotomy-healing-in-an-experimental-rat-model-of-type-i-diabetes-and-osteoporosis
#11
Ataroalsadat Mostafavinia, Reza Ahadi, Mohammadamin Abdollahifar, Seyed Kamran Ghorishi, Ali Jalalifirouzkouhi, Mohammad Bayat
BACKGROUND: Pulsed wave (PW) lasers exhibit biostimulatory effects on fractures in healthy and diabetic animals. OBJECTIVE: This study aims to assess the effects of photobiomodulation on bone strength and Hounsfield unit (HU) for repair of a bone defect in an experimental rat model of type I diabetes mellitus (TIDM) and osteoporosis (OP). METHODS: We divided 30 female rats into six groups of n = 5 per group: (1) ovariectomy (OVX) control, (2) OVX + PW laser and no TIDM, (3) OVX control + TIDM, (4) OVX + TIDM + PW laser, (5) OVX + TIDM + alendronate, and (6) OVX + TIDM + PW laser + alendronate...
February 22, 2017: Photomedicine and Laser Surgery
https://www.readbyqxmd.com/read/28437189/metformin-attenuates-radiation-induced-pulmonary-fibrosis-in-a-murine-model
#12
Jian Wang, Ye Wang, Jun Han, Hong Mei, Dandan Yu, Qian Ding, Tao Zhang, Gang Wu, Gang Peng, Zhenyu Lin
While radiotherapy continues to be a major cancer treatment option, its dose-limiting side effects, such as pulmonary fibrosis, severely impair the quality of life in these patients. In this study, we evaluated the radioprotective effects of metformin, a commonly used biguanide antidiabetic medication, in a murine model of pulmonary damage. Sprague Dawley(®) rats received whole lung 20 Gy irradiation with or without metformin treatment. Computed tomography (CT) was performed and Hounsfield units (HU) were determined during the observation period...
April 24, 2017: Radiation Research
https://www.readbyqxmd.com/read/28437136/enumeration-of-ancestral-configurations-for-matching-gene-trees-and-species-trees
#13
Filippo Disanto, Noah A Rosenberg
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the recursive computation of the conditional probability under the multispecies coalescent model of a gene tree topology given a species tree, the cost of this computation being affected by the number of ancestral configurations of the gene tree in the species tree. For matching gene trees and species trees, we obtain enumerative results on ancestral configurations...
April 24, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28437096/importance-of-mm-polarization-in-qm-mm-studies-of-enzymatic-reactions-assessment-of-the-qm-mm-drude-oscillator-model
#14
Abir Ganguly, Eliot Boulanger, Walter Thiel
For accurate quantum mechanics/molecular mechanics (QM/MM) studies of enzymatic reactions, it is desirable to include MM polarization, for example by using the Drude oscillator (DO) model. For a long time, such studies were hampered by the lack of well-tested polarizable force fields for proteins. Following up on a recent preliminary QM/MM-DO assessment (J. Chem. THEORY: Comput. 2014, 10, 1795-1809) we now report a comprehensive investigation of the effects of MM polarization on two enzymatic reactions, namely the Claisen rearrangement in chorismate mutase and the hydroxylation reaction in p-hydroxybenzoate hydrolase, using the QM/CHARMM-DO model and two QM methods (B3LYP, OM2)...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28436944/active-and-poised-promoter-states-drive-folding-of-the-extended-hoxb-locus-in-mouse-embryonic-stem-cells
#15
Mariano Barbieri, Sheila Q Xie, Elena Torlai Triglia, Andrea M Chiariello, Simona Bianco, Inês de Santiago, Miguel R Branco, David Rueda, Mario Nicodemi, Ana Pombo
Gene expression states influence the 3D conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation states in mouse embryonic stem (ES) cells. To predict possible folding scenarios, we performed computer simulations of polymer models informed with different chromatin occupancy features that define promoter activation states or binding sites for the transcription factor CTCF...
April 24, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28436897/tensor-factorized-neural-networks
#16
Jen-Tzung Chien, Yi-Ting Bao
The growing interests in multiway data analysis and deep learning have drawn tensor factorization (TF) and neural network (NN) as the crucial topics. Conventionally, the NN model is estimated from a set of one-way observations. Such a vectorized NN is not generalized for learning the representation from multiway observations. The classification performance using vectorized NN is constrained, because the temporal or spatial information in neighboring ways is disregarded. More parameters are required to learn the complicated data structure...
April 17, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28436869/establishing-keypoint-matches-on-multimodal-images-with-bootstrap-strategy-and-global-information
#17
Yong Li, Hongbin Jin, Jiatao Wu, Jie Liu
This paper proposes an algorithm of building keypoint matches on multimodal images by combining a bootstrap process and global information. The correct ratio of keypoint matches built with descriptors is typically very low on multimodal images of large spectral difference. To identify correct matches, global information is utilized for evaluating keypoint matches and a bootstrap technique is employed to reduce the computational cost. A keypoint match determines a transformation T and a similarity metric between the reference and the transformed test image by T...
April 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28436868/high-order-local-pooling-and-encoding-gaussians-over-a-dictionary-of-gaussians
#18
Peihua Li, Hui Zeng, Qilong Wang, Simon Shiu, Lei Zhang
Local pooling (LP) in configuration (feature) space proposed by Boureau et al. explicitly restricts similar features to be aggregated, which can preserve as much discriminative information as possible. At the time it appeared, this method combined with sparse coding achieved competitive classification results with only a small dictionary. However, its performance lags far behind state-of-the-art results as only zero-order information is exploited. Inspired by the success of high-order statistical information in existing advanced feature coding or pooling methods, we make an attempt to address the limitation of LP...
April 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28436847/learning-trans-dimensional-random-fields-with-applications-to-language-modeling
#19
Bin Wang, Zhijian Ou, Zhiqiang Tan
To describe trans-dimensional observations in sample spaces of different dimensions, we propose a probabilistic model, called the trans-dimensional random field (TRF) by explicitly mixing a collection of random fields. In the framework of stochastic approximation (SA), we develop an effective training algorithm, called augmented SA, which jointly estimates the model parameters and normalizing constants while using trans-dimensional mixture sampling to generate observations of different dimensions. Furthermore, we introduce several statistical and computational techniques to improve the convergence of the training algorithm and reduce computational cost, which together enable us to successfully train TRF models on large datasets...
April 24, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28436840/a-parametric-computational-model-of-the-action-potential-of-pacemaker-cells
#20
Weiwei Ai, Nitish Patel, Partha Roop, Avinash Malik, Sidharta Andalam, Eugene Yip, Nathan Allen, Mark Trew
OBJECTIVE: A flexible, efficient and verifiable pacemaker cell model is essential to the design of real-time virtual hearts that can be used for closed-loop validation of cardiac devices. A new parametric model of pacemaker action potential is developed to address this need. METHODS: The action potential phases are modeled using hybrid automaton (HA) with one piecewise-linear continuous variable. The model can capture ratedependent dynamics, such as action potential duration (APD) restitution, conduction velocity (CV) restitution, and overdrive suppression by incorporating non-linear update functions...
April 24, 2017: IEEE Transactions on Bio-medical Engineering
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