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https://www.readbyqxmd.com/read/28335582/nonradiative-relaxation-mechanisms-of-uv-excited-phenylalanine-residues-a-comparative-computational-study
#1
Momir Mališ, Nađa Došlić
The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory...
March 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335540/a-vehicle-steering-recognition-system-based-on-low-cost-smartphone-sensors
#2
Xinhua Liu, Huafeng Mei, Huachang Lu, Hailan Kuang, Xiaolin Ma
Recognizing how a vehicle is steered and then alerting drivers in real time is of utmost importance to the vehicle and driver's safety, since fatal accidents are often caused by dangerous vehicle maneuvers, such as rapid turns, fast lane-changes, etc. Existing solutions using video or in-vehicle sensors have been employed to identify dangerous vehicle maneuvers, but these methods are subject to the effects of the environmental elements or the hardware is very costly. In the mobile computing era, smartphones have become key tools to develop innovative mobile context-aware systems...
March 20, 2017: Sensors
https://www.readbyqxmd.com/read/28335218/aggregation-and-colloidal-stability-of-commercially-available-al%C3%A2-o%C3%A2-nanoparticles-in-aqueous-environments
#3
Julie Mui, Jennifer Ngo, Bojeong Kim
The aggregation and colloidal stability of three, commercially-available, gamma-aluminum oxide nanoparticles (γ-Al₂O₃ NPs) (nominally 5, 10, and 20-30 nm) were systematically examined as a function of pH, ionic strength, humic acid (HA) or clay minerals (e.g., montmorillonite) concentration using dynamic light scattering and transmission electron microscopy techniques. NPs possess pH-dependent surface charges, with a point of zero charge (PZC) of pH 7.5 to 8. When pH < PZC, γ-Al₂O₃ NPs are colloidally stable up to 100 mM NaCl and 30 mM CaCl₂...
May 13, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335215/rapamycin-loaded-solid-lipid-nanoparticles-as-a-new-tool-to-deliver-mtor-inhibitors-formulation-and-in-vitro-characterization
#4
Alice Polchi, Alessandro Magini, Jarosław Mazuryk, Brunella Tancini, Jacek Gapiński, Adam Patkowski, Stefano Giovagnoli, Carla Emiliani
Recently, the use of mammalian target of rapamycin (mTOR) inhibitors, in particular rapamycin (Rp), has been suggested to improve the treatment of neurodegenerative diseases. However, as Rp is a strong immunosuppressant, specific delivery to the brain has been postulated to avoid systemic exposure. In this work, we fabricated new Rp loaded solid lipid nanoparticles (Rp-SLN) stabilized with polysorbate 80 (PS80), comparing two different methods and lipids. The formulations were characterized by differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR), wide angle X-ray scattering (WAXS), cryo-transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS) and particle tracking...
May 9, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334816/dynamic-changes-in-chromatin-states-during-specification-and-differentiation-of-adult-intestinal-stem-cells
#5
Juri Kazakevych, Sergi Sayols, Berith Messner, Christina Krienke, Natalia Soshnikova
Epigenetic mechanisms, including chromatin structure, chromatin dynamics and histone modifications play an important role for maintenance and differentiation of pluripotent embryonic stem cells. However, little is known about the molecular mechanisms of adult stem cell specification and differentiation. Here, we used intestinal stem cells (ISCs) as a model system to reveal the epigenetic changes coordinating gene expression programs during these processes. We found that two distinct epigenetic mechanisms participate in establishing the transcriptional program promoting ISC specification from embryonic progenitors...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334758/n1-methyl-pseudouridine-in-mrna-enhances-translation-through-eif2%C3%AE-dependent-and-independent-mechanisms-by-increasing-ribosome-density
#6
Yuri V Svitkin, Yi Min Cheng, Tirtha Chakraborty, Vladimir Presnyak, Matthias John, Nahum Sonenberg
Certain chemical modifications confer increased stability and low immunogenicity to in vitro transcribed mRNAs, thereby facilitating expression of therapeutically important proteins. Here, we demonstrate that N1-methyl-pseudouridine (N1mΨ) outperforms several other nucleoside modifications and their combinations in terms of translation capacity. Through extensive analysis of various modified transcripts in cell-free translation systems, we deconvolute the different components of the effect on protein expression independent of mRNA stability mechanisms...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334697/constraint-based-stoichiometric-modelling-from-single-organisms-to-microbial-communities
#7
REVIEW
Willi Gottstein, Brett G Olivier, Frank J Bruggeman, Bas Teusink
Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28334667/redox-controlled-release-dynamics-of-thallium-in-periodically-flooded-arable-soil
#8
Svetlana Antić-Mladenović, Tina Frohne, Mirjana Kresović, Hans-Joachim Stärk, Dubravka Savić, Vlado Ličina, Jörg Rinklebe
To our knowledge, this is the first work to mechanistically study the impact of the redox potential (EH) and principal factors, such as pH, iron (Fe), manganese (Mn), dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), chlorides (Cl(-)) and sulfates (SO4(2-)), on the release dynamics of thallium (Tl) in periodically flooded soil. We simulated flooding using an automated biogeochemical microcosm system that allows for systematical control of pre-defined redox windows. The EH value was increased mechanistically at intervals of approximately 100 mV from reducing (-211 mV) to oxidizing (475 mV) conditions...
March 16, 2017: Chemosphere
https://www.readbyqxmd.com/read/28334532/an-ultrafast-switchable-terahertz-polarization-modulator-based-on-iii-v-semiconductor-nanowires
#9
Sarwat A Baig, Jessica L Boland, Djamshid A Damry, Hark Hoe Tan, Chennupati Jagadish, Hannah J Joyce, Michael B Johnston
Progress in the terahertz (THz) region of the electromagnetic spectrum is undergoing major advances, with advanced THz sources and detectors being developed at a rapid pace. Yet, ultrafast THz communication is still to be realised, owing to the lack of practical and effective THz modulators. Here, we present a novel ultrafast active THz polarization modulator based on GaAs semiconductor nanowires arranged in a wire-grid configuration. We utilise an optical pump--terahertz probe spectroscopy system and vary the polarization of the optical pump beam to demonstrate ultrafast THz modulation with a switching time of less than 5\,ps and a modulation depth of -8dB...
March 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28334358/ranges-of-cervical-intervertebral-disc-deformation-during-an-in-vivo-dynamic-flexion-extension-of-the-neck
#10
Yan Yu, Haiqing Mao, Jing-Sheng Li, Tsung-Yuan Tsai, Liming Cheng, Kirkham B Wood, Guoan Li, Thomas D Cha
While abnormal loading is widely believed to cause cervical spine disc diseases, in-vivo cervical disc deformation during dynamic neck motion has not been well delineated. This study investigated the range of cervical disc deformation during an in-vivo functional flexion-extension of the neck. Ten asymptomatic human subjects were tested using a combined dual fluoroscopic imaging system and MRI based 3D modeling technique. Overall disc deformation was determined using the changes of the space geometry between upper and lower endplates of each intervertebral segment (C3/4, C4/5, C5/6 and C6/7)...
March 23, 2017: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/28334318/laboratory-and-field-age-of-aqueous-grape-juice-bait-and-capture-of-zaprionus-indianus-diptera-drosophilidae
#11
Nancy D Epsky, Micah A Gill
Volatile chemicals produced by actively fermenting aqueous grape juice bait have been found to be highly attractive to the African fig fly, Zaprionus indianus Gupta. This is a highly dynamic system and time period of fermentation is an important factor in bait efficacy. A series of field tests were conducted that evaluated effects of laboratory versus field fermentation and sampling period (days after placement [DAP]) on bait effectiveness as the first step in identifying the chemicals responsible for attraction...
March 8, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28334271/a-temperature-dependent-phenology-model-for-liriomyza-huidobrensis-diptera-agromyzidae
#12
Norma Mujica, Marc Sporleder, Pablo Carhuapoma, Jürgen Kroschel
Liriomyza huidobrensis (Blanchard) is an economically important and highly polyphagous worldwide pest. To establish a temperature-dependent phenology model, essential for understanding the development and growth of the pest population under a variety of climates and as part of a pest risk analysis, L. huidobrensis life-table data were collected under laboratory conditions at seven constant temperatures on its host faba bean (Vicia faba L.). Several nonlinear equations were fitted to each life stage to model the temperature-dependent population growth and species life history and finally compile an overall temperature-dependent pest phenology model using the Insect Life Cycle Modeling (ILCYM) software...
March 8, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28334215/systematic-inference-of-functional-phosphorylation-events-in-yeast-metabolism
#13
Yu Chen, Yonghong Wang, Jens Nielsen
Motivation: Protein phosphorylation is a post-translational modification that affects proteins by changing their structure and conformation in a rapid and reversible way, and it is an important mechanism for metabolic regulation in cells. Phosphoproteomics enables high-throughput identification of phosphorylation events on metabolic enzymes, but identifying functional phosphorylation events still requires more detailed biochemical characterization. Therefore, development of computational methods for investigating unknown functions of a large number of phosphorylation events identified by phosphoproteomics has received increased attention...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334199/stepwise-inference-of-likely-dynamic-flux-distributions-from-metabolic-time-series-data
#14
Mojdeh Faraji, Eberhard O Voit
Motivation: Most metabolic pathways contain more reactions than metabolites and therefore have a wide stoichiometric matrix that corresponds to infinitely many possible flux distributions that are perfectly compatible with the dynamics of the metabolites in a given dataset. This under-determinedness poses a challenge for the quantitative characterization of flux distributions from time series data and thus for the design of adequate, predictive models. Here we propose a method that reduces the degrees of freedom in a stepwise manner and leads to a dynamic flux distribution that is, in a statistical sense, likely to be close to the true distribution...
March 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334116/spatial-and-temporal-variability-in-the-nitrogen-cyclers-of-hypereutrophic-lake-taihu
#15
Lauren E Krausfeldt, Xiangming Tang, Jodie van de Kamp, Guang Gao, Levente Bodrossy, Gregory L Boyer, Steven W Wilhelm
Harmful cyanobacterial blooms (cyanoHABs) are a major threat to freshwater ecosystems worldwide. Evidence suggests that both nitrogen and phosphorus are important nutrients in the development and proliferation of blooms, yet much less is known about nitrogen cycling dynamics in these systems. To assess the potential nitrogen cycling function of the cyanoHAB community, surface water samples were collected in Lake Tai (Taihu), China over a 5-month bloom event in 2014. The expression of six nitrogen cycling genes (nifH, hzsA, nxrB, nrfA, amoA, nosZ) was surveyed using a targeted microarray with probes designed to provide phylogenetic information...
February 23, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334084/molecular-dynamics-recipes-for-genome-research
#16
Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer...
February 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333960/effect-of-the-dilution-rate-on-microbial-competition-r-strategist-can-win-over-k-strategist-at-low-substrate-concentration
#17
Mari-K H Winkler, Pieter Boets, Birk Hahne, Peter Goethals, Eveline I P Volcke
The conditions present in both in vitro and in vivo ecosystems determine the microbial population harbouring it. One commonly accepted theory is that a species with a high substrate affinity and low growth rate (k-strategist) will win the competition against a second species with a lower substrate affinity and higher growth rate (r-strategist) if both species are subjected to low substrate concentrations. In this study two nitrite oxidizing bacteria (NOB), Nitrospira defluvii (k-strategist) and Nitrobacter vulgaris (r-strategist), were cultivated in a continuous reactor systems...
2017: PloS One
https://www.readbyqxmd.com/read/28333652/survivability-modeling-and-resource-planning-for-self-repairing-reconfigurable-device-fabrics
#18
Rashad S Oreifej, Rawad Al-Haddad, Ramtin Zand, Rizwan A Ashraf, Ronald F DeMara
A resilient system design problem is formulated as the quantification of uncommitted reconfigurable resources required for a system of components to survive its lifetime within mission availability specifications. We show that this survivability metric can be calculated according to the residual functionality obtained from pools of dynamically configurable elements constituting the amorphous resource pool (ARP). The ARP is depleted based on the failure rate to replenish the functionality lost in a reconfigurable fabric due to the occurrence of permanent faults during the mission lifetime...
March 21, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28333650/validation-of-static-and-dynamic-balance-assessment-using-microsoft-kinect-for-young-and-elderly-populations
#19
Moataz Eltoukhy, Christopher Kuenze, Jeonghoon Oh, Joseph Signorile
Reduction in balance is an indicator of fall risk, and therefore, an accurate and cost effective balance assessment tool is essential for prescribing effective postural control strategies. This study established the validity of the Kinect v2 sensor in assessing center of mass (CoM) excursion and velocity during single leg balance and voluntary ankle sway tasks among young and elderly subjects. We compared balance outcome measures (anteroposterior (AP) and mediolateral (ML) CoM excursion and velocity and average sway length) to a traditional three-dimensional motion analysis system...
March 22, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28333591/evidence-accumulation-and-change-rate-inference-in-dynamic-environments
#20
Adrian E Radillo, Alan Veliz-Cuba, Krešimir Josić, Zachary P Kilpatrick
In a constantly changing world, animals must account for environmental volatility when making decisions. To appropriately discount older, irrelevant information, they need to learn the rate at which the environment changes. We develop an ideal observer model capable of inferring the present state of the environment along with its rate of change. Key to this computation is an update of the posterior probability of all possible change point counts. This computation can be challenging, as the number of possibilities grows rapidly with time...
March 23, 2017: Neural Computation
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