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https://www.readbyqxmd.com/read/28453624/inferring-rates-and-length-distributions-of-indels-using-approximate-bayesian-computation
#1
Eli Levy Karin, Dafna Shkedy, Haim Ashkenazy, Reed A Cartwright, Tal Pupko
The most common evolutionary events at the molecular level are single-base substitutions, and insertions and deletions of short DNA segments (indels). A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned)...
April 26, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28447976/method-of-direct-segmental-intra-hepatic-delivery-using-a-rat-liver-hilar-clamp-model
#2
Eliza W Beal, Curtis Dumond, Jung-Lye Kim, Khalid Mumtaz, Don Hayes, Ken Washburn, Bryan A Whitson, Sylvester M Black
Major hepatic surgery with inflow occlusion, and liver transplantation, necessitate a period of warm ischemia, and a period of reperfusion leading to ischemia/reperfusion (I/R) injury with myriad negative consequences. Potential I/R injury in marginal organs destined for liver transplantation contributes to the current donor shortage secondary to a decreased organ utilization rate. A significant need exists to explore hepatic I/R injury in order to mediate its impact on graft function in transplantation. Rat liver hilar clamp models are used to investigate the impact of different molecules on hepatic I/R injury...
April 2, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28445548/assessing-the-severity-of-sleep-apnea-syndrome-based-on-ballistocardiogram
#3
Zhu Wang, Xingshe Zhou, Weichao Zhao, Fan Liu, Hongbo Ni, Zhiwen Yu
BACKGROUND: Sleep Apnea Syndrome (SAS) is a common sleep-related breathing disorder, which affects about 4-7% males and 2-4% females all around the world. Different approaches have been adopted to diagnose SAS and measure its severity, including the gold standard Polysomnography (PSG) in sleep study field as well as several alternative techniques such as single-channel ECG, pulse oximeter and so on. However, many shortcomings still limit their generalization in home environment. In this study, we aim to propose an efficient approach to automatically assess the severity of sleep apnea syndrome based on the ballistocardiogram (BCG) signal, which is non-intrusive and suitable for in home environment...
2017: PloS One
https://www.readbyqxmd.com/read/28444125/sudden-cardiac-death
#4
Jagdesh Kandala, Clint Oommen, Karl B Kern
Introduction: Sudden cardiac arrest continues to be the leading cause of death in the industrialized world. Sources of data: Original papers, reviews and guidelines. Areas of agreement: Community programs for lay bystander cardiopulmonary resuscitation (CPR) and automatic external defibrillation improve outcomes. Post-arrest care, including targeted temperature management (TTM) combined with early coronary angiography and percutaneous coronary intervention, is helpful for those suffering cardiac arrest during an ST-segment elevation myocardial infarction...
April 24, 2017: British Medical Bulletin
https://www.readbyqxmd.com/read/28442857/influence-of-blood-flow-on-the-neuroma-formation-after-transposition-of-the-nerve-stump-into-vein-experimental-and-clinical-study
#5
Hossam El-Din Ali Ismail, Mohamed Ali Kasem, Fatma El-Hossiney Mostafa
We study the influence of blood flow on the neuroma formation after transposition of the nerve stump into a vein. A total of 30 rats were divided into two groups. In group (I), a 10-mm segment of the femoral vein was excluded from the blood stream. A venotomy was performed in the middle of this segment. The proximal nerve stump of femoral nerve was transposed into the lumen of the femoral vein via a venotomy and held with an epineural suture through the venous wall. In group (II), the same technique was used as in group (I) but without exclusion of the vein segment from blood flow...
April 2017: Journal of Hand and Microsurgery
https://www.readbyqxmd.com/read/28442741/polarization-conversion-when-focusing-cylindrically-polarized-vortex-beams
#6
Alexey P Porfirev, Andrey V Ustinov, Svetlana N Khonina
Currently, cylindrical beams with radial or azimuthal polarization are being used successfully for the optical manipulation of micro- and nano-particles as well as in microscopy, lithography, nonlinear optics, materials processing, and telecommunication applications. The creation of these laser beams is carried out using segmented polarizing plates, subwavelength gratings, interference, or light modulators. Here, we demonstrate the conversion of cylindrically polarized laser beams from a radial to an azimuthal polarization, or vice versa, by introducing a higher-order vortex phase singularity...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28440471/time-dependent-differential-expression-of-long-non-coding-rnas-following-peripheral-nerve-injury
#7
Bin Pan, Heng-Xing Zhou, Yi Liu, Jia-Yin Yan, Yao Wang, Xue Yao, Yan-Qiu Deng, Shu-Yi Chen, Lu Lu, Zhi-Jian Wei, Xiao-Hong Kong, Shi-Qing Feng
Long non-coding RNAs (lncRNAs) are widely accepted as key players in various biological processes. However, the roles of lncRNA in peripheral nerve regeneration remain completely unknown. Thus, in this study, we performed microarray analysis to measure lncRNA expression in the distal segment of the sciatic nerve at 0, 3, 7 and 14 days following injury. We identified 5,354 lncRNAs that were differentially expressed: 3,788 lncRNAs were differentially expressed between days 0 and 3; 3,314 lncRNAs were differentially expressed between days 0 and 7; and 2,400 lncRNAs were differentially expressed between days 0 and 14...
April 21, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28437634/convolutional-neural-network-regression-for-short-axis-left-ventricle-segmentation-in-cardiac-cine-mr-sequences
#8
Li Kuo Tan, Yih Miin Liew, Einly Lim, Robert A McLaughlin
Automated left ventricular (LV) segmentation is crucial for efficient quantification of cardiac function and morphology to aid subsequent management of cardiac pathologies. In this paper, we parameterize the complete (all short axis slices and phases) LV segmentation task in terms of the radial distances between the LV centerpoint and the endo- and epicardial contours in polar space. We then utilize convolutional neural network regression to infer these parameters. Utilizing parameter regression, as opposed to conventional pixel classification, allows the network to inherently reflect domain-specific physical constraints...
April 12, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28437575/the-24-segment-sphericity-index-a-new-technique-to-evaluate-fetal-cardiac-diastolic-shape
#9
Greggory R DeVore, Berthold Klas, Gary Satou, Mark Sklansky
INTRODUCTION: Because of parallel circulation in the fetus and the differential effect various disease states may have on the shape of the right and left ventricles, this study was conducted to evaluate the Sphericity Index (SI) of 24 transverse segments distributed from the base to the apex of the ventricular chambers. METHODS: Two hundred control fetuses were examined between 20 and 40 weeks of gestation. The displacement of the ventricular endocardium during the cardiac cycle was computed using offline software...
April 24, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28436892/godec-fast-and-robust-low-rank-matrix-decomposition-based-on-maximum-correntropy
#10
Kailing Guo, Liu Liu, Xiangmin Xu, Dong Xu, Dacheng Tao
GoDec is an efficient low-rank matrix decomposition algorithm. However, optimal performance depends on sparse errors and Gaussian noise. This paper aims to address the problem that a matrix is composed of a low-rank component and unknown corruptions. We introduce a robust local similarity measure called correntropy to describe the corruptions and, in doing so, obtain a more robust and faster low-rank decomposition algorithm: GoDec+. Based on half-quadratic optimization and greedy bilateral paradigm, we deliver a solution to the maximum correntropy criterion (MCC)-based low-rank decomposition problem...
April 24, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28436850/pulmonary-lobe-segmentation-with-probabilistic-segmentation-of-the-fissures-and-a-groupwise-fissure-prior
#11
Felix Bragman, Jamie McClelland, Joseph Jacob, John Hurst, David Hawkes
A fully automated, unsupervised lobe segmentation algorithm is presented based on a probabilistic segmentation of the fissures and the simultaneous construction of a population model of the fissures. A two-class probabilistic segmentation segments the lung into candidate fissure voxels and the surrounding parenchyma. This was combined with anatomical information and a groupwise fissure prior to drive non-parametric surface fitting to obtain the final segmentation. The performance of our fissure segmentation was validated on 30 patients from the COPDGene cohort, achieving a high median F1-score of 0:90 and showed general insensitivity to filter parameters...
April 18, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28436106/therapeutic-plasma-exchange-as-part-of-multimodal-treatment-of-acquired-hemophilia-in-a-patient-with-concurrent-acute-intracerebral-bleed-and-pulmonary-embolism
#12
Geoffrey D Wool, David Chapel, Angela Treml, Jonathan L Miller
BACKGROUND: Autoantibodies against Factor VIII (FVIII) define the rare but life-threatening bleeding disorder acquired hemophilia A (AHA). Correction of FVIII deficiency and eradication of the factor inhibitor are the ultimate therapeutic goals in this disorder. Bypassing agents such as recombinant factor VIIa (rFVIIa) or FVIII inhibitor bypassing agent are often used to control coagulopathy before the inhibitor is eradicated. Bypassing agents carry a risk of thrombosis, however. CASE REPORT: We report a patient with newly diagnosed AHA and thalamic bleed who additionally had active atrial fibrillation and developed a segmental pulmonary embolism, limiting tolerable rFVIIa dosage...
April 24, 2017: Transfusion
https://www.readbyqxmd.com/read/28433627/docosahexaenoic-acid-promotes-differentiation-of-photoreceptor-cells-in-three-dimensional-neural-retinas
#13
Eisuke Arai, Vipul M Parmar, Bhubanananda Sahu, Lindsay Perusek, Tanu Parmar, Akiko Maeda
Retinal tissues generated from human pluripotent stem cells can be an excellent tool for investigating pathogenesis of retinal diseases and developing new pharmacologic therapies. Moreover, patient derived retinal tissues could allow for retinal transplantation therapy for degenerative retinal diseases. However, obtaining retinal tissues with matured photoreceptor outer segments, which are essential for photoreceptor functions, is currently challenging. Here we investigated the effects of docosahexaenoic acid (DHA) for maturation of photoreceptor outer segments at the late stage and visual chromophore analog, 9-cis-retinal for the early stage of differentiation to three-dimensional (3D)-retinal tissues from human embryonic stem cells (hESCs), respectively...
April 19, 2017: Neuroscience Research
https://www.readbyqxmd.com/read/28432113/automated-quantitative-characterisation-of-retinal-vascular-leakage-and-microaneurysms-in-ultra-widefield-fluorescein-angiography
#14
Justis P Ehlers, Kevin Wang, Amit Vasanji, Ming Hu, Sunil K Srivastava
Ultra-widefield fluorescein angiography (UWFA) is an emerging imaging modality used to characterise pathology in the retinal vasculature such as microaneurysms (MAs) and vascular leakage. Despite its potential value for diagnosis and disease surveillance, objective quantitative assessment of retinal pathology by UWFA is currently limited because it requires laborious manual segmentation by trained human graders. In this report, we describe a novel fully automated software platform, which segments MAs and leakage areas in native and dewarped UWFA images with retinal vascular disease...
April 21, 2017: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/28431023/safety-and-efficacy-of-the-sofia-6f-plus-distal-access-reperfusion-catheter-in-the-endovascular-treatment-of-acute-ischemic-stroke
#15
Hussain Shallwani, Hakeem J Shakir, Leonardo Rangel-Castilla, Jason M Davies, Ashish Sonig, Mithun G Sattur, Bernard R Bendok, Kenneth V Snyder, Adnan H Siddiqui, Elad I Levy
BACKGROUND: Neuroendovascular intervention has become a key treatment option for acute ischemic stroke. The Sofia (6F) PLUS catheter was designed for neurovascular access for diagnostic or therapeutic interventions. OBJECTIVE: To report the first series describing use of the Sofia PLUS intermediate/distal access reperfusion catheter in the treatment of acute ischemic stroke. METHODS: In this retrospective study, 41 stroke cases were identified in which the catheter was utilized for thrombolysis/thrombectomy...
April 19, 2017: Neurosurgery
https://www.readbyqxmd.com/read/28429419/semi-synthesis-of-murine-prion-protein-by-native-chemical-ligation-and-chemical-activation-for-preparation-of-polypeptide-%C3%AE-thioester
#16
Lei Shi, Huai Chen, Si-Yu Zhang, Ting-Ting Chu, Yu-Fen Zhao, Yong-Xiang Chen, Yan-Mei Li
Prions are suspected as pathogen of the fatal transmissible spongiform encephalopathies. Strategies to access homogenous prion protein (PrP) are required to fully comprehend the molecular mechanism of prion diseases. However, the polypeptide fragments from PrP show a high tendency to form aggregates, which is a gigantic obstacle of protein synthesis and purification. In this study, murine prion sequence 90 to 230 that is the core three-dimensional structure domain was constructed from three segments murine PrP (mPrP)(90-177), mPrP(178-212), and mPrP(213-230) by combining protein expression, chemical synthesis and chemical ligation...
April 21, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28428741/assessing-auditory-processing-deficits-in-tinnitus-and-hearing-impaired-patients-with-the-auditory-behavior-questionnaire
#17
Isabel Diges, Francisco Simón, Pedro Cobo
Background and Purpose: Auditory processing disorders (APD), tinnitus and hearing loss (HL) are typical issues reported by patients in audiologic clinics. These auditory impairments can be concomitant or mutually excluding. APD are not necessarily accompanied by significant HL, whereas many adults exhibit peripheral HL and typical cognitive deficits often associated with APD. Since HL, tinnitus and APD affects to several parts of the ascending auditory pathway from the periphery to the auditory cortex, there could be some interrelationship between them...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28428520/-prevention-of-spinal-cord-ischemia-during-thoracic-endovascular-aortic-repair
#18
Shinya Takahashi, Taijiro Sueda
Spinal cord ischemia(SCI) has been devastating complication of endovascular thoracic and thoracoabdominal aortic repair. Spinal cord blood supply arises from not only segmental artery, subclavian artery, hypogastric artery and these branches, but also perivertebral vasculature and paravertebral muscle and small arterial network, and risk factors of SCI were multifactorial. There are several adjuncts/strategies which are utilized to minimize the incidence of SCI: cerebrospinal fluid drainage, perioperative management of high mean arterial pressure, intraoperative evoked potential monitoring, and staged thoracoabdominal aortic repair...
April 2017: Kyobu Geka. the Japanese Journal of Thoracic Surgery
https://www.readbyqxmd.com/read/28424057/personalized-medicine-in-europe-not-yet-personal-enough
#19
Antonello Di Paolo, François Sarkozy, Bettina Ryll, Uwe Siebert
BACKGROUND: Personalized medicine has the potential to allow patients to receive drugs specific to their individual disease, and to increase the efficiency of the healthcare system. There is currently no comprehensive overview of personalized medicine, and this research aims to provide an overview of the concept and definition of personalized medicine in nine European countries. METHODS: A targeted literature review of selected health databases and grey literature was conducted to collate information regarding the definition, process, use, funding, impact and challenges associated with personalized medicine...
April 19, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28424004/segmental-diffusion-properties-of-the-corticospinal-tract-and-motor-outcome-in-hemiparetic-children-with-perinatal-stroke
#20
Jacquie Hodge, Bradley Goodyear, Helen Carlson, Xing-Chang Wei, Adam Kirton
Perinatal stroke injures developing motor systems, resulting in hemiparetic cerebral palsy. Diffusion tensor imaging can explore structural connectivity. We used diffusion tensor imaging to assess corticospinal tract diffusion in hemiparetic children with perinatal stroke. Twenty-eight children (6-18 years) with unilateral stroke underwent diffusion tensor imaging. Four corticospinal tract assessments included full tract, partial tract, minitract and region of interest. Diffusion characteristics (fractional anisotropy, mean, axial, and radial diffusivity) were calculated...
May 2017: Journal of Child Neurology
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