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https://www.readbyqxmd.com/read/30540963/axon-seq-decodes-the-motor-axon-transcriptome-and-its-modulation-in-response-to-als
#1
Jik Nijssen, Julio Aguila, Rein Hoogstraaten, Nigel Kee, Eva Hedlund
Spinal motor axons traverse large distances to innervate target muscles, thus requiring local control of cellular events for proper functioning. To interrogate axon-specific processes we developed Axon-seq, a refined method incorporating microfluidics, RNA sequencing (RNA-seq), and bioinformatic quality control. We show that the axonal transcriptome is distinct from that of somas and contains fewer genes. We identified 3,500-5,000 transcripts in mouse and human stem cell-derived spinal motor axons, most of which are required for oxidative energy production and ribogenesis...
December 11, 2018: Stem Cell Reports
https://www.readbyqxmd.com/read/30540840/developing-an-efficient-protocol-for-monitoring-eagle-fatalities-at-wind-energy-facilities
#2
Eric C Hallingstad, Paul A Rabie, Andrew C Telander, Jerry A Roppe, Laura R Nagy
Researchers typically conduct fatality monitoring to determine a wind energy facility's direct impacts on wildlife. In the United States, wind energy impacts on eagles have received increased attention in recent years because eagle incidental take permits became available. Permit holders are required to conduct fatality monitoring to evaluate compliance with permitted eagle take. Our objective was to develop an efficient eagle fatality monitoring protocol with a quantifiable detection probability based on a stationary scanning search method...
2018: PloS One
https://www.readbyqxmd.com/read/30540812/age-threshold-for-recommending-higher-protein-intake-to-prevent-age-related-muscle-weakness-a-cross-sectional-study-in-japan
#3
Hitomi Suga, Hideki Hashimoto
Although insufficient dietary protein intake is a known risk factor for age-related muscle weakness, the optimal age at which higher protein intake is required to prevent muscle weakness is yet to be determined. Using a population-based panel survey of community-dwelling people aged 50-75 years, this cross-sectional study aimed to find the age threshold at which a higher protein intake is associated with higher muscle strength. We utilized a dataset from the Japanese Study of Aging and Retirement conducted between 2007 and 2011...
2018: PloS One
https://www.readbyqxmd.com/read/30539668/sequence-effect-in-the-treatment-of-proliferative-diabetic-retinopathy-with-intravitreal-ranibizumab-and-panretinal-photocoagulation
#4
Guofan Cao, Xiangzhong Xu, Chenghu Wang, Shu Zhang
PURPOSE: To compare the outcome of the sequence in the two treatments (intravitreal ranibizumab and panretinal photocoagulation) in high-risk proliferative diabetic retinopathy. METHODS: This retrospective study included 35 patients with newly diagnosed high-risk proliferative diabetic retinopathy in 43 eyes; 18 (22 eyes) received intravitreal ranibizumab before panretinal photocoagulation (intravitreal ranibizumab+ group), while the other 17 (21 eyes) received panretinal photocoagulation before intravitreal ranibizumab (panretinal photocoagulation+ group)...
December 12, 2018: European Journal of Ophthalmology
https://www.readbyqxmd.com/read/30538673/somatotropic-axis-regulation-unravels-the-differential-effects-of-nutritional-and-environmental-factors-in-growth-performance-of-marine-farmed-fishes
#5
REVIEW
Jaume Pérez-Sánchez, Paula Simó-Mirabet, Fernando Naya-Català, Juan Antonio Martos-Sitcha, Erick Perera, Azucena Bermejo-Nogales, Laura Benedito-Palos, Josep Alvar Calduch-Giner
The Gh/Prl/Sl family has evolved differentially through evolution, resulting in varying relationships between the somatotropic axis and growth rates within and across fish species. This is due to a wide range of endogenous and exogenous factors that make this association variable throughout season and life cycle, and the present minireview aims to better define the nutritional and environmental regulation of the endocrine growth cascade over precisely defined groups of fishes, focusing on Mediterranean farmed fishes...
2018: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/30538621/mitochondrial-fission-is-required-for-blue-light-induced-apoptosis-and-mitophagy-in-retinal-neuronal-r28-cells
#6
Jia-Yu Li, Kun Zhang, Dan Xu, Wen-Tian Zhou, Wen-Qing Fang, Yu-Ying Wan, Dan-Dan Yan, Miao-Yu Guo, Jin-Xin Tao, Wen-Chuan Zhou, Fan Yang, Li-Ping Jiang, Xiao-Jian Han
Light emitting diodes (LEDs) are widely used to provide illumination due to their low energy requirements and high brightness. However, the LED spectrum contains an intense blue light component which is phototoxic to the retina. Recently, it has been reported that blue light may directly impinge on mitochondrial function in retinal ganglion cells (RGCs). Mitochondria are high dynamic organelles that undergo frequent fission and fusion events. The aim of our study was to elucidate the role of mitochondrial dynamics in blue light-induced damage in retinal neuronal R28 cells...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/30538573/altered-epidermal-fatty-acid-binding-protein-expression-in-hepatocellular-carcinoma-predicts-unfavorable-outcomes
#7
Jia-Bin Lu, Shao-Hang Cai, Ying-Hua Pan, Jing-Ping Yun
Objective: Hepatocellular carcinoma (HCC) is a rapidly proliferating malignancy that requires large amounts of fatty acids to synthesize cellular membranes and provide energy. Epidermal fatty acid-binding protein (EFABP) is uniquely expressed in epidermal cells, but its role and expression in HCC are not clear. Subjects and methods: A total of 804 HCC specimens were collected to construct a tissue microarray (TMA) and for immunohistochemistry (IHC) analysis. The relationship between EFABP expression and clinical features of patients with HCC was analyzed...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/30537957/wrist-accelerometer-shape-feature-derivation-methods-for-assessing-activities-of-daily-living
#8
Matin Kheirkhahan, Avirup Chakraborty, Amal A Wanigatunga, Duane B Corbett, Todd M Manini, Sanjay Ranka
BACKGROUND: There has been an increasing interest in understanding the usefulness of wrist-based accelerometer data for physical activity (PA) assessment due to the ease of use and higher user compliance than other body placements. PA assessment studies have relied on machine learning methods which take accelerometer data in forms of variables, or feature vectors. METHODS: In this work, we introduce automated shape feature derivation methods to transform epochs of accelerometer data into feature vectors...
December 12, 2018: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/30537822/accelerating-the-calculation-of-protein-ligand-binding-free-energy-and-residence-times-using-dynamically-optimized-collective-variables
#9
Zacharias Faidon Brotzakis, Vittorio Limongelli, Michele Parrinello
Elucidation of the ligand/protein binding interaction is of paramount relevance in pharmacology to increase the success rate of drug design. To this end a number of computational methods have been proposed, however all of them suer from limitations since the ligand binding/unbinding transitions to the molecular target involve many slow degrees of freedom that hamper a full characterization of the binding process. Being able to express this transition in simple and general slow degrees of freedom, would give a distinctive advantage, since it would require minimal knowledge of the system under study, while in turn it would elucidate its physics and accelerate the convergence speed of enhanced sampling methods relying on collective variables...
December 11, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30537694/failure-mode-in-first-principles-computational-tensile-tests-of-grain-boundaries-effects-of-a-bulk-region-size-dominant-factors-and-local-energy-and-local-stress-analysis
#10
Hao Wang, Masanori Kohyama, Shingo Tanaka, KaiJin Wang, Ying Chen
A first-principles computational tensile test (FPCTT) is a powerful tool
 to investigate intrinsic strength and failure processes of grain
 boundaries (GBs), according to atomic and
 electronic behaviors based on density-functional theory, while
 careful interpretation is required in comparison with experiments,
 because of ideal conditions used in FPCTTs. We
 observed serious effects of a bulk-region size in FPCTTs of
 the {001} Σ5 GB in Al.
 For a GB supercell with enough thick bulk regions, the energy-strain curve shows spontaneous failure with catastrophic energy release just after the maximum stress point, which we name Type-A failure...
December 11, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/30537470/efficiency-of-excitation-energy-trapping-in-the-green-photosynthetic-bacterium-chlorobaculum-tepidum
#11
Reza Ranjbar Choubeh, Rob B M Koehorst, David Bína, Paul C Struik, Jakub Pšenčík, Herbert van Amerongen
During the millions of years of evolution, photosynthetic organisms have adapted to almost all terrestrial and aquatic habitats, although some environments are obviously more suitable for photosynthesis than others. Photosynthetic organisms living in low-light conditions require on the one hand a large light-harvesting apparatus to absorb as many photons as possible. On the other hand, the excitation trapping time scales with the size of the light-harvesting system, and the longer the distance over which the formed excitations have to be transferred, the larger the probability to lose excitations...
December 8, 2018: Biochimica et biophysica acta. Bioenergetics
https://www.readbyqxmd.com/read/30537466/protein-s-glutathionylation-the-linchpin-for-the-transmission-of-regulatory-information-on-redox-buffering-capacity-in-mitochondria
#12
REVIEW
Adrian Young, Robert Gill, Ryan J Mailloux
Protein S-glutathionylation reactions are a ubiquitous oxidative modification required to control protein function in response to changes in redox buffering capacity. These reactions are rapid and reversible and are, for the most part, enzymatically mediated by glutaredoxins (GRX) and glutathione S-transferases (GST). Protein S-glutathionylation has been found to control a range of cell functions in response to different physiological cues. Although these reactions occur throughout the cell, mitochondrial proteins seem to be highly susceptible to reversible S-glutathionylation, a feature attributed to the unique physical properties of this organelle...
December 8, 2018: Chemico-biological Interactions
https://www.readbyqxmd.com/read/30537175/detection-of-no-2-down-to-one-ppb-using-ion-in-conjugation-inspired-polymer
#13
Jin Zhou, Xue-Feng Cheng, Bi-Jun Gao, Chuang Yu, Jing-Hui He, Qing-Feng Xu, Hua Li, Na-Jun Li, Dong-Yun Chen, Jian-Mei Lu
Nitrogen dioxide (NO2 ) emission has severe impact on human health and the ecological environment and effective monitoring of NO2 requires the detection limit (limit of detection) of several parts-per-billion (ppb). All organic semiconductor-based NO2 sensors fail to reach such a level. In this work, using an ion-in-conjugation inspired-polymer (poly(3,3'-diaminobenzidine-squarine, noted as PDBS) as the sensory material, NO2 can be detected as low as 1 ppb, which is the lowest among all reported organic NO2 sensors...
December 7, 2018: Small
https://www.readbyqxmd.com/read/30537130/nanoplumbing-with-2d-metamaterials
#14
Saroj Dangi, Robert Riehn
Complex manipulations of DNA in a nanofluidic device require channels with branches and junctions. However, the dynamic response of DNA in such nanofluidic networks is relatively unexplored. Here, the transport of DNA in a 2D metamaterial made by arrays of nanochannel junctions is investigated. The mechanism of transport is explained as Brownian motion through an energy landscape formed by the combination of the confinement free energy of DNA and the effective potential of hydrodynamic flow, which both can be tuned independently within the device...
December 11, 2018: Small
https://www.readbyqxmd.com/read/30536717/label-free-metabolic-classification-of-single-cells-in-droplets-using-the-phasor-approach-to-fluorescence-lifetime-imaging-microscopy
#15
Ning Ma, Gopakumar Kamalakshakurup, Mohammad Aghaamoo, Abraham P Lee, Michelle A Digman
Characterization of single cell metabolism is imperative for understanding subcellular functional and biochemical changes associated with healthy tissue development and the progression of numerous diseases. However, single-cell analysis often requires the use of fluorescent tags and cell lysis followed by genomic profiling to identify the cellular heterogeneity. Identifying individual cells in a noninvasive and label-free manner is crucial for the detection of energy metabolism which will discriminate cell types and most importantly critical for maintaining cell viability for further analysis...
December 11, 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/30536013/rapid-imaging-of-bcl-2-family-interactions-in-live-cells-using-flim-fret
#16
Elizabeth J Osterlund, Nehad Hirmiz, Christian Tardif, David W Andrews
The Bcl-2 proteins control cell death via interchanging interactions within the Bcl-2 family. Fluorescence lifetime imaging microscopy (FLIM) is used to detect Förster resonance energy transfer (FRET) between two fluorescent-fusion proteins in live cells. FLIM-FRET has been used to detect specific interactions and their disruption, for Bcl-2 family proteins. To date, this has been possible only in low throughput, due to the time required for serial data acquisition. We developed an automated optical system with eight parallel detectors for rapid and efficient data collection...
2019: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30535680/mitochondrial-involvement-in-mental-disorders-energy-metabolism-genetic-and-environmental-factors
#17
Keiko Iwata
Mental disorders such as major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SZ) are generally characterized by a combination of abnormal thoughts, perceptions, emotions, behavior, and relationships with others. Multiple risk factors incorporating genetic and environmental susceptibility are associated with development of these disorders. Mitochondria have a central role in the energy metabolism, and the literature suggests energy metabolism abnormalities are widespread in the brains of subjects with MDD, BD, and SZ...
2019: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30535631/aortic-pulse-wave-velocity-is-greater-in-peritoneal-dialysis-patients-with-lower-dual-energy-x-ray-absorptiometry-dxa-femoral-neck-bone-mineral-density
#18
Kamonwan Tangvoraphonkchai, Andrew Davenport
BACKGROUND: Increased vascular stiffness is associated with low bone mineral density (BMD) in the general population, and both are risk factors for mortality. We wished to determine whether vascular stiffness is associated with BMD in peritoneal dialysis (PD) patients. METHODS: We measured vascular stiffness by aortic pulse wave velocity (aPWV), BMD by dual electron absorptiometry (DXA) scanning, and body composition using bioimpedance. RESULTS: We reviewed DXA scans in 125 PD patients, 56...
December 10, 2018: Journal of Nephrology
https://www.readbyqxmd.com/read/30535388/impact-of-nanoparticle-clustering-on-dose-radio-enhancement
#19
Hilary Byrne, Aimee McNamara, Zdenka Kuncic
High atomic number nanoparticles (NPs) have been shown to enhance the effects of radiation in vitro and in vivo. However, NPs are often observed to cluster together, leading to inhomogeneous distribution within the tissue and within cells themselves. The effect of this clustering on the capability of NPs to enhance radiation dose has not yet been fully investigated. In this Monte Carlo simulation study, the dependence of radio-enhancement on a separation parameter characterising NP clustering was investigated...
December 10, 2018: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/30535313/evaluation-of-methods-for-generative-modeling-of-cell-and-nuclear-shape
#20
Xiongtao Ruan, Robert F Murphy
Motivation: Cell shape provides both a geometry for, and a reflection of, cell function. Numerous methods for describing and modeling cell shape have been described, but previous evaluation of these methods in terms of the accuracy of generative models has been limited. Results: Here we compare traditional methods and deep autoencoders to build generative models for cell shapes in terms of the accuracy with which shapes can be reconstructed from models. We evaluated the methods on different collections of 2D and 3D cell images, and found that none of the methods gave accurate reconstructions using low dimensional encodings...
December 7, 2018: Bioinformatics
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