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Dynamic linear model

Ciarán L Kelly, George M Taylor, Andrew Hitchcock, Antonio Torres-Méndez, John T Heap
Cyanobacteria are important for fundamental studies of photosynthesis and have great biotechnological potential. In order to better study and fully exploit these organisms, the limited repertoire of genetic tools and parts must be expanded. A small number of inducible promoters have been used in cyanobacteria, allowing dynamic external control of gene expression through the addition of specific inducer molecules. However, the inducible promoters used to date suffer from various drawbacks including toxicity of inducers, leaky expression in the absence of inducer and inducer photolability, the latter being particularly relevant to cyanobacteria which, as photoautotrophs, are grown under light...
March 15, 2018: ACS Synthetic Biology
Felix A Blyakhman, Nikita A Buznikov, Tatyana F Sklyar, Alexander P Safronov, Elizaveta V Golubeva, Andrey V Svalov, Sergey Yu Sokolov, Grigory Yu Melnikov, Iñaki Orue, Galina V Kurlyandskaya
Hydrogels are biomimetic materials widely used in the area of biomedical engineering and biosensing. Ferrogels (FG) are magnetic composites capable of functioning as magnetic field sensitive transformers and field assisted drug deliverers. FG can be prepared by incorporating magnetic nanoparticles (MNPs) into chemically crosslinked hydrogels. The properties of biomimetic ferrogels for multifunctional biosensor applications can be set up by synthesis. The properties of these biomimetic ferrogels can be thoroughly controlled in a physical experiment environment which is much less demanding than biotests...
March 15, 2018: Sensors
Michelle Livne, Jens K Boldsen, Irene K Mikkelsen, Jochen B Fiebach, Jan Sobesky, Kim Mouridsen
BACKGROUND AND PURPOSE: Stroke imaging is pivotal for diagnosis and stratification of patients with acute ischemic stroke to treatment. The potential of combining multimodal information into reliable estimates of outcome learning calls for robust machine learning techniques with high flexibility and accuracy. We applied the novel extreme gradient boosting algorithm for multimodal magnetic resonance imaging-based infarct prediction. METHODS: In a retrospective analysis of 195 patients with acute ischemic stroke, fluid-attenuated inversion recovery, diffusion-weighted imaging, and 10 perfusion parameters were derived from acute magnetic resonance imaging scans...
March 14, 2018: Stroke; a Journal of Cerebral Circulation
James Patrick Ewen, Sridhar Kumar Kannam, Billy D Todd, Daniele Dini
The slip and friction behaviour of n-hexadecane, confined between organic friction modifier (OFM) surfactant films adsorbed on hematite surfaces, have been studied using nonequilibrium molecular dynamics (NEMD) simulations. The influence of OFM type and coverage, as well as the applied shear rate and pressure have been investigated. A measurable slip length is only observed for OFM films with a high surface coverage, which provide smooth interfaces between well-defined OFM and hexadecane layers. Slip commences above a critical shear rate, beyond which the slip length first increases with increasing shear rate and then asymptotes towards a constant value...
March 14, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Cheng Wan-Ting, Pan Xiang, Yang Ya, Yang Yu, Li Lin-Han, He Zhong, Cai Bin, Wan Wei, Jiang Jie, Jiang Qing-Wu, Zhou Yi-Biao
OBJECTIVE: To explore the dynamic changes of Oncomelania hupensis snail densities in autumn and winter and the relationship between hydrological and meteorological factors and snail growth and decline. METHODS: From Octobers to Decembers of 2007 to 2014, a bottomland close to eastern Dongting Lake was selected as the study field. The snails and elevation of the points were surveyed, and the hydrological and meteorological data were collected. The snail densities and death rates of every month were calculated...
December 11, 2017: Zhongguo Xue Xi Chong Bing Fang Zhi za Zhi, Chinese Journal of Schistosomiasis Control
Rajesh B Patil, Euzebio G Barbosa, Jaiprakash N Sangshetti, Vishal P Zambre, Sanjay D Sawant
Dipeptidyl peptidase-IV (DPP-IV) inhibitors are promising antidiabetic agents. Currently, several DPP-IV inhibitors have been approved for therapeutic use in diabetes mellitus. Receptor-dependent 4D-QSAR is comparatively a new approach which uses molecular dynamics simulations to generate conformational ensemble profiles of compounds representing a dynamic state of compounds at a target's binding site. This work describes a receptor-dependent 4D-QSAR study on triazolopiperazine derivatives. QSARINS multiple linear regression method was adopted to generate 4D-QSAR models...
March 13, 2018: Molecular Diversity
Marco Pisanello, Filippo Pisano, Leonardo Sileo, Emanuela Maglie, Elisa Bellistri, Barbara Spagnolo, Gil Mandelbaum, Bernardo L Sabatini, Massimo De Vittorio, Ferruccio Pisanello
Optogenetic control of neural activity in deep brain regions ideally requires precise and flexible light delivery with non-invasive devices. To this end, Tapered Optical Fibers (TFs) represent a versatile tool that can deliver light over either large brain volumes or spatially confined sub-regions, while being sensibly smaller than flat-cleaved optical fibers. In this work, we report on the possibility of further extending light emission length along the taper in the range 0.4 mm-3.0 mm by increasing the numerical aperture of the TFs to NA = 0...
March 13, 2018: Scientific Reports
Santiago Martinez, Juan Miguel Garcia-Haro, Juan G Victores, Alberto Jardon, Carlos Balaguer
The computational complexity of humanoid robot balance control is reduced through the application of simplified kinematics and dynamics models. However, these simplifications lead to the introduction of errors that add to other inherent electro-mechanic inaccuracies and affect the robotic system. Linear control systems deal with these inaccuracies if they operate around a specific working point but are less precise if they do not. This work presents a model improvement based on the Linear Inverted Pendulum Model (LIPM) to be applied in a non-linear control system...
March 11, 2018: Sensors
Ehsan Shakeri, Gholamreza Latif-Shabgahi, Amir Esmaeili Abharian
In recent years, many efforts have been made to present optimal strategies for cancer therapy through the mathematical modelling of tumour-cell population dynamics and optimal control theory. In many cases, therapy effect is included in the drift term of the stochastic Gompertz model. By fitting the model with empirical data, the parameters of therapy function are estimated. The reported research works have not presented any algorithm to determine the optimal parameters of therapy function. In this study, a logarithmic therapy function is entered in the drift term of the Gompertz model...
April 2018: IET Systems Biology
Jonathan P Rehfuss, Kenneth M DeSart, Jared M Rozowsky, Kerri A O'Malley, Lyle L Moldawer, Henry V Baker, Yaqun Wang, Rongling Wu, Peter R Nelson, Scott A Berceli
BACKGROUND: Despite being the definitive treatment for lower extremity peripheral arterial disease, vein bypass grafts fail in half of all cases. Early repair mechanisms after implantation, governed largely by the immune environment, contribute significantly to long-term outcomes. The current study investigates the early response patterns of circulating monocytes as a determinant of graft outcome. METHODS: In 48 patients undergoing infrainguinal vein bypass grafting, the transcriptomes of circulating monocytes were analyzed preoperatively and at 1, 7, and 28 days post-operation...
March 2018: Circ Genom Precis Med
Miguel Arocena, Jorge M Pérez Zerpa, Andrés Di Paolo, Pedro A Aguilera, José Sotelo-Silveira
Cell migration involves the precise coordination between extension at the front of the cell and retraction at the rear. This coordination is particularly evident in fast moving cells such as fish keratocytes, where it leads to highly stable gliding motion, propelled at the front by broad, 0.1-0-2 μm thick lamellipodia. Transient uncoupling between extension and retraction can occur if the rear is temporarily stuck, which might eventually lead to cell shape instabilities. We have frequently observed in fish keratocytes the presence of lamellipodial radial wrinkles, detected by confocal, scanning electron and side-view microscopy as folds in the lamellipodium up to 2 μm in height...
March 9, 2018: Biochemical and Biophysical Research Communications
A I Mirulla, L Bragonzoni, S Zaffagnini, M Bontempi, V Nigrelli, T Ingrassia
INTRODUCTION: Traditional prosthetic solutions expose the amputee to numerous problems that limit his ability to safely perform the normal activities of daily life. In order to eliminate the problems related to the use of the traditional prosthesis with socket, a new technique was developed for fixing the prosthesis to the amputees based on the principle of osseointegration. The aim of this paper is to study and analyze the stress distribution on the interface between a trans-humeral osseointegrated prosthetic implant and the residual bone, identifying the most stressed areas and thus foreseeing possible failure phenomena of the entire prosthetic system and, after, to compare the stress distribution on three different prosthetic designs that differ from each other for some geometric characteristics...
March 7, 2018: Injury
Jingbo Sun, Salih Z Silahli, Wiktor Walasik, Qi Li, Eric Johnson, Natalia M Litchinitser
Colloidal media with well-defined optical properties have been widely used as model systems in many fundamental and applied studies of light-matter interactions in complex media. Recent progress in the field of engineered nanoscale optical materials with fundamentally new physical properties opens new opportunities for tailoring the properties of colloids. In this work, we experimentally demonstrate the evolution of the optical vortex beams of different topological charges propagating in engineered nano-colloidal suspension of negative polarizability with saturable nonlinearities...
March 5, 2018: Optics Express
Da Lei, Mian Lin, Yun Li, Wenbin Jiang
OBJECTIVES: An accurate model of the dynamic contact angle θd is critical for the calculation of capillary force in applications like enhanced oil recovery, where the capillary number Ca ranges from 10-10 to 10-5 and the Bond number Bo is less than 10-4 . The rate-dependence of the dynamic contact angle under such conditions remains blurred, and is the main target of this study. EXPERIMENTS: Featuring with pressure control and interface tracking, the innovative experimental system presented in this work achieves the desired ranges of Ca and Bo, and enables the direct optical measurement of dynamic contact angles in capillaries as tiny as 40 × 20 (width × height) μm and 80 × 20 μm...
March 1, 2018: Journal of Colloid and Interface Science
Sonja Cerar, Kim Mezga, Gorazd Žibret, Janko Urbanc, Marko Komac
Groundwater is the most important source of drinking water in the world. Therefore, information on the quality and quantity is important, as is new information related to the characteristics of the aquifer and the recharge area. In the present study we focused on the isotope composition of oxygen (δ18 O) in groundwater, which is a natural tracer and provides a better understanding of the water cycle, in terms of origin, dynamics and interaction. The groundwater δ18 O at 83 locations over the entire Slovenian territory was studied...
March 9, 2018: Science of the Total Environment
Mohammad Muneeb Sultan, Hannah K Wayment-Steele, Vijay S Pande
Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification that allows us to rapidly perform sampling in multiple related systems. We first demonstrate our method is able to describe the effects of force field changes in capped alanine dipeptide after learning a model using AMBER99...
March 12, 2018: Journal of Chemical Theory and Computation
Ismail Turkan, Baris Uzilday, Karl-Josef Dietz, Andrea Bräutigam, Rengin Ozgur
Redox regulation, antioxidant defence and ROS signalling are critical in realizing and tuning metabolic activities. However, our concepts were mostly developed for C3 plants since Arabidopsis thaliana is major model. Efforts to convert C3 plants to C4 plants to increase yield (see C4 rice; entails better understanding of these processes in C4 plants. Various photosynthetic enzymes that take part in light reactions and carbon reactions are regulated via redox components such as thioredoxins as redox transmitters and peroxiredoxins...
February 26, 2018: Journal of Experimental Botany
Alison Kitson, Alan Brook, Gill Harvey, Zoe Jordan, Rhianon Marshall, Rebekah O'Shea, David Wilson
Many representations of the movement of healthcare knowledge through society exist, and multiple models for the translation of evidence into policy and practice have been articulated. Most are linear or cyclical and very few come close to reflecting the dense and intricate relationships, systems and politics of organizations and the processes required to enact sustainable improvements. We illustrate how using complexity and network concepts can better inform knowledge translation (KT) and argue that changing the way we think and talk about KT could enhance the creation and movement of knowledge throughout those systems needing to develop and utilise it...
July 10, 2017: International Journal of Health Policy and Management
Alessandra H Ide, José Manuel F Nogueira
A new hybrid microextraction technique (hollow fiber microextraction) is presented that uses the main concepts and advantages of the modern miniaturized devices used for trace analysis. This novel analytical approach uses devices made of polypropylene membranes (10.0 mm long and 0.6 mm internal diameter) in which convenient organic solvents are embedded that promote fast kinetics during the enrichment process, using the floating sampling technology concept. An innovative analytical cycle is also proposed by use of low-cost disposable devices during the microextraction stage together with a user-friendly ("single liquid desorption step") back-extraction stage in compliance with green analytical chemistry principles...
March 10, 2018: Analytical and Bioanalytical Chemistry
Matic Grom, Mirijam Kozorog, Simon Caserman, Andrej Pohar, Blaž Likozar
Protein A-based affinity chromatography is a highly-efficient separation method to capture, purify and isolate biosimilar monoclonal antibodies (mAb) - an important medical product of biopharmaceutical industrial manufacturing. It is considered the most expensive step in purification downstream operations; therefore, its performance optimization offers a great cost saving in the overall production expenditure. The biochemical mixture-separating specific interaction experiments with Chinese hamster ovary (CHO) cell culture harvest, containing glycosylated extracellular immunoglobulins (Ig), were made using five different state-of-the-art commercial resins...
March 1, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
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