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https://www.readbyqxmd.com/read/28230851/using-hiclip-to-identify-rna-duplexes-that-interact-with-a-specific-rna-binding-protein
#1
Yoichiro Sugimoto, Anob M Chakrabarti, Nicholas M Luscombe, Jernej Ule
The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28228535/genome-wide-prediction-of-metabolic-enzymes-pathways-and-gene-clusters-in-plants
#2
Pascal Schlapfer, Peifen Zhang, Chuan Wang, Taehyong Kim, Michael Banf, Lee Chae, Kate Dreher, Arvind K Chavali, Ricardo Nilo-Poyanco, Thomas Bernard, Daniel Kahn, Seung Y Rhee
Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways and gene clusters from a sequenced genome...
February 22, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28228269/diverse-central-projection-patterns-of-retinal-ganglion-cells
#3
Emily M Martersteck, Karla E Hirokawa, Mariah Evarts, Amy Bernard, Xin Duan, Yang Li, Lydia Ng, Seung W Oh, Benjamin Ouellette, Joshua J Royall, Michelle Stoecklin, Quanxin Wang, Hongkui Zeng, Joshua R Sanes, Julie A Harris
Understanding how >30 types of retinal ganglion cells (RGCs) in the mouse retina each contribute to visual processing in the brain will require more tools that label and manipulate specific RGCs. We screened and analyzed retinal expression of Cre recombinase using 88 transgenic driver lines. In many lines, Cre was expressed in multiple RGC types and retinal cell classes, but several exhibited more selective expression. We comprehensively mapped central projections from RGCs labeled in 26 Cre lines using viral tracers, high-throughput imaging, and a data processing pipeline...
February 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28228131/whole-genome-sequencing-of-one-complex-pedigree-illustrates-challenges-with-genomic-medicine
#4
Han Fang, Yiyang Wu, Hui Yang, Margaret Yoon, Laura T Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang, Gholson J Lyon
BACKGROUND: Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. METHODS: We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader-Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms...
February 23, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28227996/a-novel-approach-for-chewing-detection-based-on-a-wearable-ppg-sensor
#5
Vasileios Papapanagiotou, Christos Diou, Lingchuan Zhou, Janet van den Boer, Monica Mars, Anastasios Delopoulos, Vasileios Papapanagiotou, Christos Diou, Lingchuan Zhou, Janet van den Boer, Monica Mars, Anastasios Delopoulos, Janet van den Boer, Vasileios Papapanagiotou, Lingchuan Zhou, Anastasios Delopoulos, Monica Mars, Christos Diou
Monitoring of human eating behaviour has been attracting interest over the last few years, as a means to a healthy lifestyle, but also due to its association with serious health conditions, such as eating disorders and obesity. Use of self-reports and other non-automated means of monitoring have been found to be unreliable, compared to the use of wearable sensors. Various modalities have been reported, such as acoustic signal from ear-worn microphones, or signal from wearable strain sensors. In this work, we introduce a new sensor for the task of chewing detection, based on a novel photoplethysmography (PPG) sensor placed on the outer earlobe to perform the task...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227849/smartphone-based-real-time-speech-enhancement-for-improving-hearing-aids-speech-perception
#6
Yu Rao, Yiya Hao, Issa M S Panahi, Nasser Kehtarnavaz, Yu Rao, Yiya Hao, Issa M S Panahi, Nasser Kehtarnavaz, Yu Rao, Issa M S Panahi, Yiya Hao, Nasser Kehtarnavaz
In this paper, the development of a speech processing pipeline on smartphones for hearing aid devices (HADs) is presented. This pipeline is used for noise suppression and speech enhancement (SE) to improve speech quality and intelligibility. The proposed method is implemented to run in real-time on Android smartphones. The results of the testing conducted indicate that the proposed method suppresses the noise and improves the perceptual quality of speech in terms of three objective measures of perceptual evaluation of speech quality (PESQ), noise attenuation level (NAL), and the coherent speech intelligibility index (CSD)...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227795/simplified-realistic-human-head-model-for-simulating-tumor-treating-fields-ttfields
#7
Cornelia Wenger, Ze'ev Bomzon, Ricardo Salvador, Peter J Basser, Pedro C Miranda, Cornelia Wenger, Ze'ev Bomzon, Ricardo Salvador, Peter J Basser, Pedro C Miranda, Peter J Basser, Pedro C Miranda, Cornelia Wenger, Ricardo Salvador, Ze'ev Bomzon
Tumor Treating Fields (TTFields) are alternating electric fields in the intermediate frequency range (100-300 kHz) of low-intensity (1-3 V/cm). TTFields are an anti-mitotic treatment against solid tumors, which are approved for Glioblastoma Multiforme (GBM) patients. These electric fields are induced non-invasively by transducer arrays placed directly on the patient's scalp. Cell culture experiments showed that treatment efficacy is dependent on the induced field intensity. In clinical practice, a software called NovoTal(TM) uses head measurements to estimate the optimal array placement to maximize the electric field delivery to the tumor...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227418/automatic-pneumonia-detection-based-on-ultrasound-video-analysis
#8
Pedro Cisneros-Velarde, Malena Correa, Holger Mayta, Cynthia Anticona, Monica Pajuelo, Richard Oberhelman, William Checkley, Robert H Gilman, Dante Figueroa, Mirko Zimic, Roberto Lavarello, Benjamin Castaneda, Pedro Cisneros-Velarde, Malena Correa, Holger Mayta, Cynthia Anticona, Monica Pajuelo, Richard Oberhelman, William Checkley, Robert H Gilman, Dante Figueroa, Mirko Zimic, Roberto Lavarello, Benjamin Castaneda, Robert H Gilman, Holger Mayta, Monica Pajuelo, Cynthia Anticona, Roberto Lavarello, Dante Figueroa, Pedro Cisneros-Velarde, Richard Oberhelman, Mirko Zimic, Benjamin Castaneda, William Checkley, Malena Correa
Pneumonia is a disease which causes high mortality in children under five years old, particularly in developing countries. This paper proposes a novel application of ultrasound video analysis for the detection of pneumonia. This application is based on the processing of small video chunks, in which an image processing algorithm analyzes each frame to get some overall video statistics. Then, based on these quantities, the likeness of presence of pneumonia in the video is determined. The algorithm exploits different geometrical properties of typical anatomical and pathological features that commonly appear in lung sonography and which are already clinically typified in the literature...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227414/breast-lesion-detection-and-characterization-with-3d-features
#9
Arathi Sreekumari, K S Shriram, Vivek Vaidya, Arathi Sreekumari, K S Shriram, Vivek Vaidya, Vivek Vaidya, K S Shriram, Arathi Sreekumari
Automated Breast Ultrasound (ABUS) is highly effective as breast cancer screening adjunct technology. Automation can greatly enhance the efficiency of the clinician sifting through the quantum of data in ABUS volumes to spot lesions. We have implemented a fully automatic generic algorithm pipeline for detection and characterization of lesions on such 3D volumes. We compare a wide range of features for region description on their effectiveness at the dual goals of lesion detection and characterization. On multiple feature images, we compute region descriptors at lesion candidate locations obviating the need for explicit lesion segmentation...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227409/projected-current-density-comparison-in-tdcs-block-and-smooth-fe-modeling
#10
Aprinda Indahlastari, Munish Chauhan, Rosalind J Sadleir, Aprinda Indahlastari, Munish Chauhan, Rosalind J Sadleir, Aprinda Indahlastari, Munish Chauhan, Rosalind J Sadleir
Current density distribution and projected current density calculation following transcranial direct current stimulation (tDCS) forward model in a human head were compared between two modeling pipelines: block and smooth. Block model was directly constructed from MRI voxel resolution and simulated in C. Smooth models underwent a boundary smoothing process by applying recursive Gaussian filters and simulated in COMSOL. Three smoothing levels were added to determine their effects on current density distribution compared to block models...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227380/efficient-rendering-of-digitally-reconstructed-radiographs-on-heterogeneous-computing-architectures-using-central-slice-theorem
#11
Marwan Abdellah, Mohamed Abdallah, Mohamed Alzanati, Ayman Eldeib, Marwan Abdellah, Mohamed Abdallah, Mohamed Alzanati, Ayman Eldeib, Ayman Eldeib, Mohamed Abdallah, Mohamed Alzanati, Marwan Abdellah
Digitally reconstructed radiographs (DRRs) play a significant role in modern clinical radiation therapy. They are used to verify patient alignments during image guided therapies with 2D-3D image registration. The generation of DRRs can be implemented intuitively in O(N(3)) relying on direct volume rendering (DVR) methods, such as ray marching. This complexity imposes certain limitations on the rendering performance if high quality DRR images are needed. Those DRRs can be alternatively generated in the k-space using the central slice theorem in O(N(2)logN)...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227379/parallel-generation-of-digitally-reconstructed-radiographs-on-heterogeneous-multi-gpu-workstations
#12
Marwan Abdellah, Asem Abdelaziz, E M B S Eslam Ali, Sherief Abdelaziz, Abdelrahman Sayed, Mohamed I Owis, Ayman Eldeib, Marwan Abdellah, Asem Abdelaziz, E M B S Eslam Ali, Sherief Abdelaziz, Abdelrahman Sayed, Mohamed I Owis, Ayman Eldeib, Sherief Abdelaziz, Mohamed I Owis, Abdelrahman Sayed, Marwan Abdellah, Asem Abdelaziz, Eslam Ali, Ayman Eldeib
The growing importance of three-dimensional radiotherapy treatment has been associated with the active presence of advanced computational workflows that can simulate conventional x-ray films from computed tomography (CT) volumetric data to create digitally reconstructed radiographs (DRR). These simulated x-ray images are used to continuously verify the patient alignment in image-guided therapies with 2D-3D image registration. The present DRR rendering pipelines are quite limited to handle huge imaging stacks generated by recent state-of-the-art CT imaging modalities...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227375/motion-invariant-contrast-enhancement-of-optical-imaging-data-in-the-gradient-domain
#13
Philipp Flotho, Alejandro Romero-Santiago, Karsten Schwerdtfeger, Jacek Szczygielski, Matthias Hulser, Lars Haab, Daniel J Strauss, Philipp Flotho, Alejandro Romero-Santiago, Karsten Schwerdtfeger, Jacek Szczygielski, Matthias Hulser, Lars Haab, Daniel J Strauss, Daniel J Strauss, Alejandro Romero-Santiago, Jacek Szczygielski, Karsten Schwerdtfeger, Philipp Flotho, Lars Haab
Functional optical imaging (OI) of intrinsic signals (like blood oxygenation coupled reflection changes) and of extrinsic properties of voltage sensitive probes (like voltage-sensitive dyes (VSD)) forms a group of neuroimaging techniques that possess up to date highest temporal and spatial resolution on a meso-to macroscopic scale. An inherent problem of OI is a very low signal to noise ratio (SNR), which restricts the recordings to be completely motionless and requires detailed knowledge of the properties of the different noise sources...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226774/modeling-non-clinical-and-clinical-drug-tests-in-gaucher-disease
#14
Clyde F Phelix, Allen K Bourdon, Greg Villareal, Richard G LeBaron, Clyde F Phelix, Allen K Bourdon, Greg Villareal, Richard G LeBaron, Richard G LeBaron, Clyde F Phelix, Allen K Bourdon, Greg Villareal
There is need for modeling biological systems to accelerate drug pipelines for treating metabolic diseases. The eliglustat treatment for Gaucher disease is approved by the FDA with a companion genomic test. The Transcriptome-To-Metabolome™ biosimulation technology was used to model, in silico, a standard non-clinical eliglustat test with an in vitro canine kidney cell system over-expressing a human gene; and a clinical test using human fibroblasts from control and Gaucher disease subjects. Protein homology modeling and docking studies were included to gather affinity parameters for the kinetic metabolic model...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226752/classification-of-sd-oct-volumes-with-multi-pyramids-lbp-and-hog-descriptors-application-to-dme-detections
#15
Khaled Alsaih, Guillaume Lemaitre, Join Massich Vall, Mojdeh Rastgoo, Desire Sidibe, Tien Y Wong, Ecosse Lamoureux, Dan Milea, Carol Y Cheung, Fabrice Meriaudeau, Khaled Alsaih, Guillaume Lemaitre, Join Massich Vall, Mojdeh Rastgoo, Desire Sidibe, Tien Y Wong, Ecosse Lamoureux, Dan Milea, Carol Y Cheung, Fabrice Meriaudeau, Guillaume Lemaitre, Dan Milea, Carol Y Cheung, Desire Sidibe, Ecosse Lamoureux, Join Massich Vall, Mojdeh Rastgoo, Fabrice Meriaudeau, Tien Y Wong, Khaled Alsaih
This paper deals with the automated detection of Diabetic Macular Edema (DME) on Optical Coherence Tomography (OCT) volumes. Our method considers a generic classification pipeline with preprocessing for noise removal and flattening of each B-Scan. Features such as Histogram of Oriented Gradients (HOG) and Local Binary Patterns (LBP) are extracted and combined to create a set of different feature vectors which are fed to a linear-Support Vector Machines (SVM) Classifier. Experimental results show a promising sensitivity/specificity of 0...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226639/an-initial-investigation-into-the-real-time-conversion-of-facial-surface-emg-signals-to-audible-speech
#16
Lorenz Diener, Christian Herff, Matthias Janke, Tanja Schultz, Lorenz Diener, Christian Herff, Matthias Janke, Tanja Schultz, Lorenz Diener, Christian Herff, Matthias Janke, Tanja Schultz
This paper presents early-stage results of our investigations into the direct conversion of facial surface electromyographic (EMG) signals into audible speech in a real-time setting, enabling novel avenues for research and system improvement through real-time feedback. The system uses a pipeline approach to enable online acquisition of EMG data, extraction of EMG features, mapping of EMG features to audio features, synthesis of audio waveforms from audio features and output of the audio waveforms via speakers or headphones...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226633/autonomous-vision-guided-approach-for-the-analysis-and-grading-of-vertical-suspension-tests-during-hammersmith-infant-neurological-examination-hine
#17
Prasenjit Dey, Debi Prosad Dogra, Partha Pratim Roy, Harish Bhaskar, Prasenjit Dey, Debi Prosad Dogra, Partha Pratim Roy, Harish Bhaskar, Debi Prosad Dogra, Harish Bhaskar, Prasenjit Dey, Partha Pratim Roy
Computer vision assisted diagnostic systems are gaining popularity in different healthcare applications. This paper presents a video analysis and pattern recognition framework for the automatic grading of vertical suspension tests on infants during the Hammersmith Infant Neurological Examination (HINE). The proposed vision-guided pipeline applies a color-based skin region segmentation procedure followed by the localization of body parts before feature extraction and classification. After constrained localization of lower body parts, a stick-diagram representation is used for extracting novel features that correspond to the motion dynamic characteristics of the infant's leg movements during HINE...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226616/a-real-time-hybrid-neuron-network-for-highly-parallel-cognitive-systems
#18
Gerrit Jan Christiaanse, Amir Zjajo, Carlo Galuzzi, Rene van Leuken, Gerrit Jan Christiaanse, Amir Zjajo, Carlo Galuzzi, Rene van Leuken, Carlo Galuzzi, Gerrit Jan Christiaanse, Rene van Leuken, Amir Zjajo
For comprehensive understanding of how neurons communicate with each other, new tools need to be developed that can accurately mimic the behaviour of such neurons and neuron networks under `real-time' constraints. In this paper, we propose an easily customisable, highly pipelined, neuron network design, which executes optimally scheduled floating-point operations for maximal amount of biophysically plausible neurons per FPGA family type. To reduce the required amount of resources without adverse effect on the calculation latency, a single exponent instance is used for multiple neuron calculation operations...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226603/automatic-switching-between-noise-classification-and-speech-enhancement-for-hearing-aid-devices
#19
Fatemeh Saki, Nasser Kehtarnavaz, Fatemeh Saki, Nasser Kehtarnavaz, Fatemeh Saki, Nasser Kehtarnavaz
This paper presents a voice activity detector (VAD) for automatic switching between a noise classifier and a speech enhancer as part of the signal processing pipeline of hearing aid devices. The developed VAD consists of a computationally efficient feature extractor and a random forest classifier. Previously used signal features as well as two newly introduced signal features are extracted and fed into the classifier to perform automatic switching. This switching approach is compared to two popular VADs. The results obtained indicate the introduced approach outperforms these existing approaches in terms of both detection rate and processing time...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226597/a-node-wise-analysis-of-the-uterine-muscle-networks-for-pregnancy-monitoring
#20
N Nader, M Hassan, W Falou, C Marque, M Khalil, N Nader, M Hassan, W Falou, C Marque, M Khalil, M Khalil, W Falou, C Marque, M Hassan, N Nader
The recent past years have seen a noticeable increase of interest in the correlation analysis of electrohysterographic (EHG) signals in the perspective of improving the pregnancy monitoring. Here we propose a new approach based on the functional connectivity between multichannel (4×4 matrix) EHG signals recorded from the women's abdomen. The proposed pipeline includes i) the computation of the statistical couplings between the multichannel EHG signals, ii) the characterization of the connectivity matrices, computed by using the imaginary part of the coherence, based on the graph-theory analysis and iii) the use of these measures for pregnancy monitoring...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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