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https://www.readbyqxmd.com/read/28110499/dynamic-predictions-using-flexible-joint-models-of-longitudinal-and-time-to-event-data
#1
Jessica Barretta, Li Sub
Joint models for longitudinal and time-to-event data are particularly relevant to many clinical studies where longitudinal biomarkers could be highly associated with a time-to-event outcome. A cutting-edge research direction in this area is dynamic predictions of patient prognosis (e.g., survival probabilities) given all available biomarker information, recently boosted by the stratified/personalized medicine initiative. As these dynamic predictions are individualized, flexible models are desirable in order to appropriately characterize each individual longitudinal trajectory...
January 22, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28110496/heterogenic-response-of-prokaryotes-toward-silver-nanoparticles-and-ions-is-facilitated-by-phenotypes-and-attachment-of-silver-aggregates-to-cell-surfaces
#2
Yuting Guo, Hans J Stärk, Gerd Hause, Matthias Schmidt, Hauke Harms, Lukas Y Wick, Susann Müller
Tons of anthropogenic silver nanoparticles (AgNPs) are assumed to be released into the environment due to their use in many consumer products. AgNPs are known to be toxic toward microorganisms and thus may harm their specific functions in ecosystems. Here we explore the impact of AgNPs on functioning of single cells in microbial populations at doses typically found in anthropogenic environments. The response of single cells to AgNPs was analyzed by flow cytometry and using the fluorescent dyes propidium iodide and DiBAC4 (3) as markers for cell membrane disintegration and depolarization, respectively...
January 22, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28110471/depletion-of-mitofusin-2-causes-mitochondrial-damage-in-cisplatin-induced-neuropathy
#3
Ilja Bobylev, Abhijeet R Joshi, Mohammed Barham, Wolfram F Neiss, Helmar C Lehmann
Sensory neuropathy is a relevant side effect of the antineoplastic agent cisplatin. Mitochondrial damage is assumed to play a critical role in cisplatin-induced peripheral neuropathy, but the pathomechanisms underlying cisplatin-induced mitotoxicity and neurodegeneration are incompletely understood. In an animal model of cisplatin-induced neuropathy, we determined in detail the extent and spatial distribution of mitochondrial damage during cisplatin treatment. Changes in the total number of axonal mitochondria during cisplatin treatment were assessed in intercostal nerves from transgenic mice that express cyan fluorescent protein...
January 21, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28110455/influence-of-environmental-and-anthropogenic-factors-at-the-bottom-sediments-in-a-doce-river-tributary-in-brazil
#4
Deyse Almeida Dos Reis, Aníbal da Fonseca Santiago, Laura Pereira Nascimento, Hubert Mathias Peter Roeser
In developing countries, it is uncommon to find watersheds that have been the object of detailed environmental studies. It makes the assessment of the magnitude of environmental impacts and pollution of these sites difficult. This research demonstrated ways to understand the dynamics of river bottom sediments contamination, even for watersheds with a lack of environmental data. Based on geochemical affinity, we conducted a comprehensive study on the concentration of metals and metalloids. Then, we discussed the probable origin of the concentration of these elements at the bottom sediment along the Matipó River...
January 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28110451/the-importance-of-various-stages-of-succession-in-preservation-of-biodiversity-among-riparian-birds-in-northern-iran
#5
Zahra Sepehri Roshan, Sina Anushiravani, Soroor Karimi, Hossein Varasteh Moradi, Abdol Rasoul Salmanmahini
Every stage of succession may provide certain species with habitat requirements which are impossible in other stages of succession. This study attempts to evaluate the different stages of succession in terms of composition and structure of bird populations in Hyrcanian forests. Bird-habitat relationships were investigated by comparing vegetation characteristics in three successional stages including late, initial stage, and urban areas. Bird richness, diversity, and abundance were measured within a 25-m radius of each of the 120 sampling points in various stages of succession and urban areas from May to April (2014) in the Ziarat catchment...
February 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28110448/molecular-dynamics-exploration-of-the-binding-mechanism-and-properties-of-single-walled-carbon-nanotube-to-wt-and-mutant-vp35-fbp-region-of-ebola-virus
#6
Yan-Jun Zhang, Jing-Na Ding, Hui Zhong, Chang-Ping Sun, Ju-Guang Han
VP35 of Ebola viruses (EBOVs) is an attractive potential target because of its multifunction. All-atom molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculations are performed to investigate the single-walled carbon nanotube (SWCNT) as an inhibitor in wild-type (WT) VP35 as well as in three primary mutants (K248A, I295A, and K248A/I295A) through docking the SWCNT in the first basic patch (FBP) of VP35. The SWCNTs of all the four systems effectively bind to the FBP...
January 21, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28110403/delayed-asymptomatic-coil-migrations-toward-different-arteries-after-aneurysmal-embolization-case-report
#7
Tomoya Kamide, Kouichi Misaki, Iku Nambu, Masanao Mohri, Naoyuki Uchiyama, Mitsutoshi Nakada
Delayed coil migration after endovascular treatment with detachable coils, particularly several months after treatment, is extremely rare. In this report, the authors describe a 77-year-old female in whom delayed coil migration to the anterior cerebral artery and posterior communicating artery (PCoA) developed 3 months after an uncomplicated aneurysm embolization. The patient was successfully retreated with a closed-cell stent. Computational fluid dynamics (CFD) revealed high wall shear stress (WSS) and multiple vortices in the residual cavity of the initially treated aneurysm...
January 21, 2017: Acta Neurochirurgica
https://www.readbyqxmd.com/read/28110354/molecular-modelling-approaches-for-the-analysis-of-histamine-receptors-and-their-interaction-with-ligands
#8
Andrea Strasser, Hans-Joachim Wittmann
Several experimental techniques to analyse histamine receptors are available, e.g. pharmacological characterisation of known or new compounds by different types of assays or mutagenesis studies. To obtain insights into the histamine receptors on a molecular and structural level, crystal structures have to be determined and molecular modelling studies have to be performed. It is widely accepted to generate homology models of the receptor of interest based on an appropriate crystal structure as a template and to refine the resulting models by molecular dynamic simulations...
January 22, 2017: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/28110351/determining-lead-cadmium-and-mercury-in-cosmetics-using-sweeping-via-dynamic-chelation-by-capillary-electrophoresis
#9
Kuan-Ling Chen, Shiuh-Jen Jiang, Yen-Ling Chen
International limits have been established for metal impurities in cosmetics to prevent overexposure to heavy metal ions. Sweeping via dynamic chelation was developed using capillary electrophoresis to analyze lead (Pb), cadmium (Cd) and mercury (Hg) impurities in cosmetics. The sweeping via dynamic chelation mechanism involves a large volume of metal ions being swept by a small quantity of chelating agents that were electrokinetically injected into the capillary to chelate metal ions and increase the detection sensitivity...
January 21, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28110274/c4-photosynthesis-50-years-of-discovery-and-innovation
#10
EDITORIAL
Susanne von Caemmerer, Oula Ghannoum, Robert T Furbank
It is now over half a century since the biochemical characterization of the C4 photosynthetic pathway, and this special issue highlights the sheer breadth of current knowledge. New genomic and transcriptomic information shows that multi-level regulation of gene expression is required for the pathway to function, yet we know it to be one of the most dynamic examples of convergent evolution. Now, a focus on the molecular transition from C3-C4 intermediates, together with improved mathematical models, experimental tools and transformation systems, holds great promise for improving C4 photosynthesis in crops...
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110273/shifting-balance-on-a-static-mutation-selection-landscape-a-novel-scenario-of-positive-selection
#11
Christopher T Jones, Noor Youssef, Edward Susko, Joseph P Bielawski
A version of the mechanistic mutation-selection (MutSel) model that accounts for temporal dynamics at a site is presented. This is used to show that the rate ratio dN/dS at a site can be transiently >1 even when fitness coefficients are fixed or the fitness landscape is static. This occurs whenever a site drifts away from its fitness peak and is then forced back by selection, a process reminiscent of shifting balance. Shifting balance is strongest when the substitution process is not dominated by selection or drift, but admits interplay between the two...
November 8, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28110263/multi-mhz-micro-electro-mechanical-sensors-for-atomic-force-microscopy
#12
Bernard Legrand, Jean-Paul Salvetat, Benjamin Walter, Marc Faucher, Didier Théron, Jean-Pierre Aimé
Silicon ring-shaped micro-electro-mechanical resonators have been fabricated and used as probes for dynamic atomic force microscopy (AFM) experiments. They offer resotnance frequency above 10MHz, which is notably greater than that of usual cantilevers and quartz-based AFM probes. On-chip electrical actuation and readout of the tip oscillation are obtained by means of built-in capacitive transducers. Displacement and force resolutions have been determined from noise analysis at 1.5fm/√Hz and 0.4 pN/√Hz, respectively...
January 12, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28110185/computational-analysis-of-amsacrine-resistance-in-human-topoisomerase-ii-alpha-mutants-r487k-and-e571k-using-homology-modeling-docking-and-all-atom-molecular-dynamics-simulation-in-explicit-solvent
#13
Safaa Sader, Chun Wu
Amsacrine is an effective topoisomerase II enzyme inhibitor in acute lymphatic leukemia. Previous experimental studies have successfully identified two important mutations (R487K and E571K) conferring 100 and 25 fold resistance to Amsacrine respectively. Although the reduction of the cleavage ligand-DNA-protein ternary complex has been well thought as the major cause of drug resistance, the detailed energetic, structural and dynamic mechanisms remain to be elusive. In this study, we constructed human topoisomerase II alpha (hTop2α) homology model docked with Amsacrine based on crystal structure of human Top2β in complex with etoposide...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28110184/structural-analysis-of-binding-functionality-of-folic-acid-peg-dendrimers-against-folate-receptor
#14
Diana Sampogna-Mireles, Ingrid D Araya-Durán, Valeria Márquez-Miranda, Jesús A Valencia-Gallegos, Fernando D González-Nilo
Dendrimers functionalized with folic acid (FA) are drug delivery systems that can selectively target cancer cells with folate receptors (FR-α) overexpression. Incorporation of polyethylene glycol (PEG) can enhance dendrimers solubility and pharmacokinetics, but ligand-receptor binding must not be affected. In this work we characterized, at atomic level, the binding functionality of conventional site-specific dendrimers conjugated with FA with PEG 750 or PEG 3350 as a linker. After Molecular Dynamics simulation, we observed that both PEG's did not interfere over ligand-receptor binding functionality...
January 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28110181/dynamic-measurement-of-surface-strain-distribution-on-the-foot-during-walking
#15
Kohta Ito, Kosuke Maeda, Ikumi Fujiwara, Koh Hosoda, Takeo Nagura, Taeyong Lee, Naomichi Ogihara
To clarify the mechanism underlying the development of foot disorders such as diabetic ulcers and deformities, it is important to understand how the foot surface elongates and contracts during gait. Such information is also helpful for improving the prevention and treatment of foot disorders. We therefore measured temporal changes in the strain distribution on the foot surface during human walking. Five adult male participants walked across a glass platform placed over an angled mirror set in a wooden walkway at a self-selected speed and the dorsolateral and plantar surfaces of the foot were filmed using two pairs of synchronized high-speed cameras...
December 18, 2016: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28110179/analysis-the-effect-of-different-geometries-of-afm-s-cantilever-on-the-dynamic-behavior-and-the-critical-forces-of-three-dimensional-manipulation
#16
Moharam Habibnejad Korayem, Maniya B Saraie, Mahdieh B Saraee
An important challenge when using an atomic force microscope (AFM) is to be able to control the force exerted by the AFM for performing various tasks. Nevertheless, the exerted force is proportional to the deflection of the AFM cantilever, which itself is affected by a cantilever's stiffness coefficient. Many papers have been published so far on the methods of obtaining the stiffness coefficients of AFM cantilevers in 2D; however, a comprehensive model is yet to be presented on 3D cantilever motion. The discrepancies between the equations of the 2D and 3D analysis are due to the number and direction of forces and moments that are applied to a cantilever...
January 13, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28110178/tem-sample-preparation-by-femtosecond-laser-machining-and-ion-milling-for-high-rate-tem-straining-experiments
#17
Thomas Voisin, Michael D Grapes, Yong Zhang, Nicholas Lorenzo, Jonathan Ligda, Brian Schuster, Timothy P Weihs
To model mechanical properties of metals at high strain rates, it is important to visualize and understand their deformation at the nanoscale. Unlike post mortem Transmission Electron Microscopy (TEM), which allows one to analyze defects within samples before or after deformation, in situ TEM is a powerful tool that enables imaging and recording of deformation and the associated defect motion during mechanical loading. Unfortunately, all current in situ TEM mechanical testing techniques are limited to quasi-static strain rates...
December 5, 2016: Ultramicroscopy
https://www.readbyqxmd.com/read/28110128/application-of-a-breakthrough-biosorbent-for-removing-heavy-metals-from-synthetic-and-real-wastewaters-in-a-lab-scale-continuous-fixed-bed-column
#18
Atefeh Abdolali, Huu Hao Ngo, Wenshan Guo, John L Zhou, Jian Zhang, Shuang Liang, Soon W Chang, Dinh Duc Nguyen, Yi Liu
A continuous fixed-bed study was carried out utilising a breakthrough biosorbent, specifically multi-metal binding biosorbent (MMBB) for removing cadmium, copper, lead and zinc. The effect of operating conditions, i.e. influent flow rate, metal concentration and bed depth was investigated at pH 5.5±0.1 for a synthetic wastewater sample. Results confirmed that the total amount of metal adsorption declined with increasing influent flow rate and also rose when each metal concentration also increased. The maximum biosorption capacities of 38...
January 10, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28110092/cutin-synthase2-maintains-progressively-developing-cuticular-ridges-in-arabidopsis-sepals
#19
Lilan Hong, Joel Brown, Nicholas A Segerson, Jocelyn K C Rose, Adrienne H K Roeder
The cuticle is a crucial barrier on the aerial surfaces of land plants. In many plants, including Arabidopsis, the sepals and petals form distinctive nanoridges in their cuticles. Yet little is known about how the formation and maintenance of these nanostructures is coordinated with the growth and development of the underlying cells. Here we characterize the cutin synthase 2 (cus2) mutant, which causes a great reduction in cuticular ridges on the mature sepal epidermis, but only a moderate effect on petal cone cell ridges...
January 18, 2017: Molecular Plant
https://www.readbyqxmd.com/read/28110068/a-photoresponsive-soft-interface-reversibly-controls-wettability-and-cell-adhesion-by-conformational-changes-in-a-spiropyran-conjugated-amphiphilic-block-copolymer
#20
Di He, Yoshinori Arisaka, Kenichi Masuda, Mitsuya Yamamoto, Naoya Takeda
: The functionalities of soft interfaces including cell adhesion can be enhanced by dynamic conversion of polymer properties and movement via external stimuli. Light is a superior stimulus, and various surfaces modified with photoreactive molecules have been prepared. However, in most of these studies, the surface properties are irreversibly changed due to photo-degradation, and reversible adhesion and collection of cells is not feasible. In this study, we developed a photoresponsive polymer soft interface that was able to spatiotemporally control wettability, cell adhesion, and detachment in a reversible manner...
January 18, 2017: Acta Biomaterialia
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