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https://www.readbyqxmd.com/read/28334390/seqarray-a-storage-efficient-high-performance-data-format-for-wgs-variant-calls
#1
Xiuwen Zheng, Stephanie M Gogarten, Michael Lawrence, Adrienne Stilp, Matthew P Conomos, Bruce S Weir, Cathy Laurie, David Levine
Motivation: Whole-genome sequencing (WGS) data is being generated at an unprecedented rate. Analysis of WGS data requires a flexible data format to store the different types of DNA variation. Variant call format (VCF) is a general text-based format developed to store variant genotypes and their annotations. However, VCF files are large and data retrieval is relatively slow. Here we introduce a new WGS variant data format implemented in the R/Bioconductor package "SeqArray" for storing variant calls in an arrayoriented manner which provides the same capabilities as VCF, but with multiple high compression options and data access using high-performance parallel computing...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28320658/compressed-sensing-based-synthetic-transmit-aperture-imaging-validation-in-a-convex-array-configuration
#2
Jing Liu, Qiong He, Jianwen Luo
According to the linear acoustic theory, the channel data of a plane wave emitted by a linear array is a linear combination of the full dataset of synthetic transmit aperture (STA). Combining this relationship with compressed sensing (CS), a novel CS based ultrasound beamforming strategy, named compressed sensing based synthetic transmit aperture (CS-STA), was previously proposed to increase the frame rate of ultrasound imaging without sacrificing the image quality for a linear array. In this paper, assuming linear transfer function of pulse-echo ultrasound system, we derived and applied the theory of CS-STA for a slightly curved array and validated CS-STA in a convex array configuration...
March 14, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28318948/comparative-assessment-of-intrinsic-mechanical-stimuli-on-knee-cartilage-and-compressed-agarose-constructs
#3
A Completo, C Bandeiras, F Fonseca
A well-established cue for improving the properties of tissue-engineered cartilage is mechanical stimulation. However, the explicit ranges of mechanical stimuli that correspond to favorable metabolic outcomes are elusive. Usually, these outcomes have only been associated with the applied strain and frequency, an oversimplification that can hide the fundamental relationship between the intrinsic mechanical stimuli and the metabolic outcomes. This highlights two important key issues: the firstly is related to the evaluation of the intrinsic mechanical stimuli of native cartilage; the second, assuming that the intrinsic mechanical stimuli will be important, deals with the ability to replicate them on the tissue-engineered constructs...
March 17, 2017: Medical Engineering & Physics
https://www.readbyqxmd.com/read/28304353/phase-error-correction-for-approximated-observation-based-compressed-sensing-radar-imaging
#4
Bo Li, Falin Liu, Chongbin Zhou, Yuanhao Lv, Jingqiu Hu
Defocus of the reconstructed image of synthetic aperture radar (SAR) occurs in the presence of the phase error. In this work, a phase error correction method is proposed for compressed sensing (CS) radar imaging based on approximated observation. The proposed method has better image focusing ability with much less memory cost, compared to the conventional approaches, due to the inherent low memory requirement of the approximated observation operator. The one-dimensional (1D) phase error correction for approximated observation-based CS-SAR imaging is first carried out and it can be conveniently applied to the cases of random-frequency waveform and linear frequency modulated (LFM) waveform without any a priori knowledge...
March 17, 2017: Sensors
https://www.readbyqxmd.com/read/28302996/spinal-cord-ischemia-secondary-to-epidural-metastasis-from-small-cell-lung-carcinoma
#5
Hirotoshi Yasui, Naoya Ozawa, Satoshi Mikami, Kenji Shimizu, Takahiro Hatta, Nami Makino, Mayu Fukushima, Satoshi Baba, Yasushi Makino
BACKGROUND Spinal cord ischemia is an uncommon event that is mainly caused by dissociation of the ascending aorta as a complication after aortic surgery. Spinal arteries can develop collateral circulation; therefore, the frequency of spinal infarction is about 1% of that in the brain. Few cases of spinal cord ischemia developing in the course of lung cancer have been reported. CASE REPORT We presented the case of a 56-year-old man with small cell lung carcinoma, cT4N2M1a (stage IV). He was treated with irradiation and 2 courses of platinum and etoposide combination chemotherapy...
March 17, 2017: American Journal of Case Reports
https://www.readbyqxmd.com/read/28300272/compressed-single-pixel-imaging-in-the-spatial-frequency-domain
#6
Mohammad Torabzadeh, Il-Yong Park, Randy A Bartels, Anthony J Durkin, Bruce J Tromberg
No abstract text is available yet for this article.
March 1, 2017: Journal of Biomedical Optics
https://www.readbyqxmd.com/read/28298767/airway-management-in-patients-with-tracheal-compression-undergoing-thyroidectomy-a-retrospective-analysis
#7
Binu Sajid, K Rekha
BACKGROUND: Airway management in large and retrosternal goiters with tracheal compression is often fraught with challenges and is a source of apprehension among anesthesiologists globally. AIMS: In this study we attempt to delineate the preferred techniques of airway management of such cases in our institution and also to assess whether airway management was unnecessarily complicated. SETTING AND DESIGN: Retrospective analysis. MATERIALS AND METHODS: A retrospective review was conducted of thyroidectomies performed in our institution over a three year period from January 2013...
January 2017: Anesthesia, Essays and Researches
https://www.readbyqxmd.com/read/28297990/laser-pulse-compression-using-magnetized-plasmas
#8
Yuan Shi, Hong Qin, Nathaniel J Fisch
Proposals to reach the next generation of laser intensities through Raman or Brillouin backscattering have centered on optical frequencies. Higher frequencies are beyond the range of such methods mainly due to the wave damping that accompanies the higher-density plasmas necessary for compressing higher frequency lasers. However, we find that an external magnetic field transverse to the direction of laser propagation can reduce the required plasma density. Using parametric interactions in magnetized plasmas to mediate pulse compression, both reduces the wave damping and alleviates instabilities, thereby enabling higher frequency or lower intensity pumps to produce pulses at higher intensities and longer durations...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297304/evaluation-of-kidney-motion-and-target-localization-in-abdominal-sbrt-patients
#9
Marcus Sonier, William Chu, Nafisha Lalani, Darby Erler, Patrick Cheung, Renee Korol
The purpose of this study was to evaluate bilateral kidney and target translational/rotational intrafraction motion during stereotactic body radiation therapy treatment delivery of primary renal cell carcinoma and oligometastatic adrenal lesions for patients immobilized in the Elekta BodyFIX system. Bilateral kidney motion was assessed at midplane for 30 patients immobilized in a full-body dual-vacuum-cushion system with two patients immobilized via abdominal compression. Intrafraction motion was assessed for 15 patients using kilovoltage cone-beam computed tomography (kV-CBCT) datasets (n=151) correlated to the planning CT...
November 2016: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28293752/acoustic-emission-signatures-during-failure-of-vertebra-and-long-bone
#10
Brian D Goodwin, Frank A Pintar, Narayan Yoganandan
Clinical classification of an injury has traditionally involved medical imaging, patient history, and physical examination. The pathogenesis or process of injury has been viewed as a crucial component to estimating fracture stability and direct treatment. However, injury classification systems generally exclude pathogenesis and injury mechanisms because these components are often difficult to elucidate. Furthermore, the development of bone damage relative to the mechanical response is difficult to quantify, which limits the ability to define injury and develop injury criteria...
March 14, 2017: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/28293486/sacral-insufficiency-fractures-recognition-and-treatment-in-patients-with-concurrent-lumbar-vertebral-compression-fractures
#11
Jesse Hatgis, Michelle Granville, Robert E Jacobson, Aldo Berti
INTRODUCTION: In reviewing a larger group of osteoporotic vertebral compression fractures (VCFs), we found that the overall incidence of sacral insufficiency fractures (SIFs) is higher than commonly reported values. This is especially seen in patients with previous or concurrent lumbar VCFs and also in a subgroup that had lumbar stenosis or hip arthroplasty. The altered biomechanics due to associated lumbar stenosis or hip arthroplasty lead to increased mechanical stress on already weakened and deficient sacral alae, which are more vulnerable to osteoporotic weakening than other parts of the sacrum...
February 2, 2017: Curēus
https://www.readbyqxmd.com/read/28293198/fetal-heart-rate-analysis-for-automatic-detection-of-perinatal-hypoxia-using-normalized-compression-distance-and-machine-learning
#12
Óscar Barquero-Pérez, Ricardo Santiago-Mozos, José M Lillo-Castellano, Beatriz García-Viruete, Rebeca Goya-Esteban, Antonio J Caamaño, José L Rojo-Álvarez, Carlos Martín-Caballero
Accurate identification of Perinatal Hypoxia from visual inspection of Fetal Heart Rate (FHR) has been shown to have limitations. An automated signal processing method for this purpose needs to deal with time series of different lengths, recording interruptions, and poor quality signal conditions. We propose a new method, robust to those issues, for automated detection of perinatal hypoxia by analyzing the FHR during labor. Our system consists of several stages: (a) time series segmentation; (b) feature extraction from FHR signals, including raw time series, moments, and usual heart rate variability indices; (c) similarity calculation with Normalized Compression Distance, which is the key element for dealing with FHR time series; and (d) a simple classification algorithm for providing the hypoxia detection...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28287424/keloid-and-hypertrophic-scars-are-the-result-of-chronic-inflammation-in-the-reticular-dermis
#13
REVIEW
Rei Ogawa
Keloids and hypertrophic scars are caused by cutaneous injury and irritation, including trauma, insect bite, burn, surgery, vaccination, skin piercing, acne, folliculitis, chicken pox, and herpes zoster infection. Notably, superficial injuries that do not reach the reticular dermis never cause keloidal and hypertrophic scarring. This suggests that these pathological scars are due to injury to this skin layer and the subsequent aberrant wound healing therein. The latter is characterized by continuous and histologically localized inflammation...
March 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28274815/electroacupuncture-improves-gait-locomotion-h-reflex-and-ventral-root-potentials-of-spinal-compression-injured-rats
#14
Carlos Escobar-Corona, Sergio Torres-Castillo, Erika Elizabeth Rodríguez-Torres, Bertha Segura-Alegría, Ismael Jiménez-Estrada, Salvador Quiroz-González
This study explored the effect of electroacupuncture stimulation (EA) on alterations in the Hoffman reflex (H-reflex) response and gait locomotion provoked by spinal cord injury (SCI) in the rat. A compression lesion of the spinal cord was evoked by insufflating a Fogarty balloon located in the epidural space at the T8-9 spinal level of adult Wistar male rats (200-250 gr; n=60). In different groups of SCI rats, EA (frequencies: 2, 50 and 100Hz) was applied simultaneously to Huantiao (GB30), Yinmen (BL37), Jizhong (GV6) and Zhiyang (GV9) acupoints from the third post-injury day until the experimental session...
March 6, 2017: Brain Research Bulletin
https://www.readbyqxmd.com/read/28269061/low-complexity-prediction-of-frequency-rich-biosignals-for-lossless-compression-in-wearable-technologies
#15
Guangwei Chen, Stuart A Bowyer, Esther Rodriguez-Villegas
Wearable technologies that store, monitor and analyse a range of biosignals are an area of significant growth and interest for both industry and academia. The rate of data generation in these devices poses a considerable challenge with regards to the bandwidths of wireless transmission protocols, local storage capacities and the on-board power consumption requirements. This issue is particularly acute for frequency-rich biosignals containing significant higher frequency components that are un-served by conventional compression techniques...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28268366/low-rank-magnetic-resonance-fingerprinting
#16
Gal Mazor, Lior Weizman, Assaf Tal, Yonina C Eldar
Magnetic Resonance Fingerprinting (MRF) is a relatively new approach that provides quantitative MRI using randomized acquisition. Extraction of physical quantitative tissue values is preformed off-line, based on acquisition with varying parameters and a dictionary generated according to the Bloch equations. MRF uses hundreds of radio frequency (RF) excitation pulses for acquisition, and therefore high under-sampling ratio in the sampling domain (k-space) is required. This under-sampling causes spatial artifacts that hamper the ability to accurately estimate the quantitative tissue values...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28265623/computational-study-of-phononic-resonators-and-waveguides-in-monolayer-transition-metal-dichalcogenides
#17
A Konstantopoulou, A P Sgouros, M M Sigalas
Using molecular dynamics and semi-empirical potentials, large scale transition metal dichalcogenides monolayers (TMDM) were examined. The focus of the study was the modification of the phonon spectrum of TMDMs by engineering substitutional defects to produce phononic resonators and waveguides on the atomic scale. The resonant frequencies of the aforementioned structures can be tuned by applying tensile or compressive stresses. The TMDMs exhibited wide phononic band gaps (PBG) in their phonon spectrum because they consist of atoms with quite different atomic masses...
March 7, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28259264/mri-screening-in-operative-scheuermann-kyphosis-is-it-necessary
#18
Baron S Lonner, Courtney S Toombs, Michael Mechlin, Gina Ciavarra, Suken A Shah, Amer F Samdani, Paul Sponseller, Harry L Shufflebarger, Randal R Betz, Burt Yaszay, Peter O Newton
STUDY DESIGN: Patients with preoperative spine magnetic resonance imaging (MRI) studies from a prospective multicenter study of operative adolescent Scheuermann kyphosis (SK). OBJECTIVES: To investigate the usefulness of MRI screening in operative planning for SK surgeries. SUMMARY OF BACKGROUND DATA: Neural axis abnormalities in operative SK have not been previously studied with MRI screening, despite its use. METHODS: One orthopedic surgeon and two radiologists evaluated all images retrospectively...
March 2017: Spine Deformity
https://www.readbyqxmd.com/read/28258771/acoustic-behavior-of-halobacterium-salinarum-gas-vesicles-in-the-high-frequency-range-experiments-and-modeling
#19
Emmanuel Cherin, Johan M Melis, Raymond W Bourdeau, Melissa Yin, Dennis M Kochmann, F Stuart Foster, Mikhail G Shapiro
Gas vesicles (GVs) are a new and unique class of biologically derived ultrasound contrast agents with sub-micron size whose acoustic properties have not been fully elucidated. In this study, we investigated the acoustic collapse pressure and behavior of Halobacterium salinarum gas vesicles at transmit center frequencies ranging from 12.5 to 27.5 MHz. The acoustic collapse pressure was found to be above 550 kPa at all frequencies, nine-fold higher than the critical pressure observed under hydrostatic conditions...
March 1, 2017: Ultrasound in Medicine & Biology
https://www.readbyqxmd.com/read/28258484/corpuls-cpr-resuscitation-device-generates-superior-emulated-flows-and-pressures-than-lucas-ii-in-a-mechanical-thorax-model
#20
S Eichhorn, A Mendoza Garcia, M Polski, J Spindler, A Stroh, M Heller, R Lange, M Krane
The provision of sufficient chest compression is among the most important factors influencing patient survival during cardiopulmonary resuscitation (CPR). One approach to optimize the quality of chest compressions is to use mechanical-resuscitation devices. The aim of this study was to compare a new device for chest compression (corpuls cpr) with an established device (LUCAS II). We used a mechanical thorax model consisting of a chest with variable stiffness and an integrated heart chamber which generated blood flow dependent on the compression depth and waveform...
March 3, 2017: Australasian Physical & Engineering Sciences in Medicine
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