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https://www.readbyqxmd.com/read/28919854/pranas-a-new-platform-for-retinal-analysis-and-simulation
#1
Bruno Cessac, Pierre Kornprobst, Selim Kraria, Hassan Nasser, Daniela Pamplona, Geoffrey Portelli, Thierry Viéville
The retina encodes visual scenes by trains of action potentials that are sent to the brain via the optic nerve. In this paper, we describe a new free access user-end software allowing to better understand this coding. It is called PRANAS (https://pranas.inria.fr), standing for Platform for Retinal ANalysis And Simulation. PRANAS targets neuroscientists and modelers by providing a unique set of retina-related tools. PRANAS integrates a retina simulator allowing large scale simulations while keeping a strong biological plausibility and a toolbox for the analysis of spike train population statistics...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28916961/practical-computational-toolkits-for-dendrimers-and-dendrons-structure-design
#2
Nuno Martinho, Liana C Silva, Helena F Florindo, Steve Brocchini, Teresa Barata, Mire Zloh
Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures...
September 15, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28903001/open-source-assisted-laboratory-automation-through-graphical-user-interfaces-and-3d-printers-application-to-equipment-hyphenation-for-higher-order-data-generation
#3
Gabriel Germán Siano, Milagros Montemurro, Mirta Raquel Alcaráz, Hector Casimiro Goicoechea
In the current analytical chemistry, even though the modeling of higher-order data can result attractive, the generation of this kind of data implies some automation challenges, which are mainly related to the hidden programming languages and electronic details of the equipment. When techniques and/or equipment hyphenation is the key to obtain higher-order data, the required simultaneous control of them demands funds for new hardware, software and licenses, and also really skilled operators. In this work we present Design of Inputs-Outputs with Sikuli (D...
September 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28891217/reproducibility-of-f18-fdg-pet-radiomic-features-for-different-cervical-tumor-segmentation-methods-gray-level-discretization-and-reconstruction-algorithms
#4
Baderaldeen A Altazi, Geoffrey G Zhang, Daniel C Fernandez, Michael E Montejo, Dylan Hunt, Joan Werner, Matthew C Biagioli, Eduardo G Moros
Site-specific investigations of the role of radiomics in cancer diagnosis and therapy are emerging. We evaluated the reproducibility of radiomic features extracted from (18) Flourine-fluorodeoxyglucose ((18) F-FDG) PET images for three parameters: manual versus computer-aided segmentation methods, gray-level discretization, and PET image reconstruction algorithms. Our cohort consisted of pretreatment PET/CT scans from 88 cervical cancer patients. Two board-certified radiation oncologists manually segmented the metabolic tumor volume (MTV1 and MTV2 ) for each patient...
September 11, 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28889357/the-development-of-skull-prosthesis-through-active-contour-model
#5
Yi-Wen Chen, Cheng-Ting Shih, Chen-Yang Cheng, Yu-Cheng Lin
Skull defects result in brain infection and inadequate brain protection and pose a general danger to patient health. To avoid these situations and prevent re-injury, a prosthesis must be constructed and grafted onto the deficient region. With the development of rapid customization through additive manufacturing and 3D printing technology, skull prostheses can be fabricated accurately and efficiently prior to cranioplasty. However, an unfitted skull prosthesis made with a metal implant can cause repeated infection, potentially necessitating secondary surgery...
September 9, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28884596/3d-map-modelling-for-the-melting-points-prediction-of-intumescent-flame-retardant-coatings
#6
A S Korotkov, M Gravit
The applicability of 3D map modelling for melting point prediction was studied. The melting points in the ammonium polyphosphate-pentaerythritol-melamine chemical system of intumescent flame-retardant coatings over a wide range of concentrations were collected. The ternary diagram (triangle) of the melting points was plotted and an approximated 3D map was built for the range 205-345°C. The present work contains the thermal data for the observed ternary system and provides a new graphic system for making predictions for intumescent flame-retardant coatings...
September 8, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28874991/ceramic-molar-crown-reproducibility-by-digital-workflow-manufacturing-an-in-vitro-study
#7
Ii-Do Jeong, Woong-Chul Kim, Jinyoung Park, Chong-Myeong Kim, Ji-Hwan Kim
PURPOSE: This in vitro study aimed to analyze and compare the reproducibility of zirconia and lithium disilicate crowns manufactured by digital workflow. MATERIALS AND METHODS: A typodont model with a prepped upper first molar was set in a phantom head, and a digital impression was obtained with a video intraoral scanner (CEREC Omnicam; Sirona GmbH), from which a single crown was designed and manufactured with CAD/CAM into a zirconia crown and lithium disilicate crown (n=12)...
August 2017: Journal of Advanced Prosthodontics
https://www.readbyqxmd.com/read/28874736/genfire-a-generalized-fourier-iterative-reconstruction-algorithm-for-high-resolution-3d-imaging
#8
Alan Pryor, Yongsoo Yang, Arjun Rana, Marcus Gallagher-Jones, Jihan Zhou, Yuan Hung Lo, Georgian Melinte, Wah Chiu, Jose A Rodriguez, Jianwei Miao
Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28871407/in-vitro-antimicrobial-susceptibility-testing-methods-agar-dilution-to-3d-tissue-engineered-models
#9
REVIEW
A Schumacher, T Vranken, A Malhotra, J J C Arts, P Habibovic
In the field of orthopaedic surgery, bacterial invasion of implants and the resulting periprosthetic infections are a common and unresolved problem. Antimicrobial susceptibility testing methods help to define the optimal treatment and identify antimicrobial resistance. This review discusses proven gold-standard techniques and recently developed models for antimicrobial susceptibility testing, while also providing a future outlook. Conventional, gold-standard methods, such as broth microdilution, are still widely applied in clinical settings...
September 4, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28871402/a-smartphone-colorimetric-reader-integrated-with-an-ambient-light-sensor-and-a-3d-printed-attachment-for-on-site-detection-of-zearalenone
#10
Yuan Chen, Qiangqiang Fu, Dagang Li, Jun Xie, Dongxu Ke, Qifang Song, Yong Tang, Hong Wang
Smartphone biosensors could be cost-effective, portable instruments to be used for the readout of liquid colorimetric assays. However, current reported smartphone colorimetric readers have relied on photos of liquid assays captured using a camera, and then analyzed using software programs. This approach results in a relatively low accuracy and low generality. In this work, we reported a novel smartphone colorimetric reader that has been integrated with an ambient light sensor and a 3D printed attachment for the readout of liquid colorimetric assays...
September 4, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28861624/docking-assisted-3d-qsar-studies-on-xanthones-as-%C3%AE-glucosidase-inhibitors
#11
Xuehua Zheng, Siyuan Zhou, Chen Zhang, Deyan Wu, Hai-Bin Luo, Yinuo Wu
Recently, a series of xanthone analogues has been identified as α-glucosidase inhibitors. To provide deeper insight into the three-dimensional (3D) structural requirements for the activities of these molecules, CoMFA and CoMSIA approaches were employed on 54 xanthones to construct 3D-QSAR models. Their bioactive conformations were first investigated by docking studies and optimized by subsequent molecular dynamics (MD) simulations using the homology modeled structure of the target protein. Based on the docking/MD-determined conformers, 3D-QSAR studies generated several significant models in terms of 47 molecules as the training set...
August 31, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28857244/rhorix-an-interface-between-quantum-chemical-topology-and-the-3d-graphics-program-blender
#12
Matthew J L Mills, Kenneth L Sale, Blake A Simmons, Paul L A Popelier
Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available...
August 31, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28852787/exploring-the-binding-of-two-potent-anticancer-drugs-bosutinib-and-imatinib-mesylate-with-bovine-serum-albumin-spectroscopic-and-molecular-dynamic-simulation-studies
#13
Suma K Pawar, Roopa S Naik, J Seetharamappa
Bosutinib (BST) and imatinib mesylate (IMT) are tyrosine kinase inhibitors (TKIs). In view of the importance of these inhibitors in cancer treatment, we investigated the mechanism of interaction between BST/IMT and bovine serum albumin (BSA) using various spectroscopic and molecular docking methods. Fluorescence studies indicated that BST/IMT interacted with BSA without affecting the microenvironment around the residue Trp213 of BSA. The quenching mechanism associated with the BST-BSA and IMT-BSA interactions was determined by performing fluorescence measurements at different temperatures...
August 29, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28808803/a-prototype-educational-model-for-hepatobiliary-interventions-unveiling-the-role-of-graphic-designers-in-medical-3d-printing
#14
Ramin Javan, Merissa N Zeman
In the context of medical three-dimensional (3D) printing, in addition to 3D reconstruction from cross-sectional imaging, graphic design plays a role in developing and/or enhancing 3D-printed models. A custom prototype modular 3D model of the liver was graphically designed depicting segmental anatomy of the parenchyma containing color-coded hepatic vasculature and biliary tree. Subsequently, 3D printing was performed using transparent resin for the surface of the liver and polyamide material to develop hollow internal structures that allow for passage of catheters and wires...
August 14, 2017: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/28801757/dft-study-of-the-interactions-between-thiophene-based-corrosion-inhibitors-and-an-fe4-cluster
#15
Duy Quang Dao, Truong Dinh Hieu, Thong Le Minh Pham, Dinh Tuan, Pham Cam Nam, Ime Bassey Obot
Understanding the physicochemical properties of corrosion inhibitors and their chemical interactions with metal surfaces is crucial to the design of improved (i.e., more efficient) corrosion inhibitors. In this work, the physicochemical properties of six thiophene-based corrosion inhibitors (2-acetylthiophene (AT), 2-formylthiophene (FT), thiophene (Th), 2-methyl-3-thiophenthiol (MTT), 2-pentylthiophene (PT), and 2-thenylthiol (TT)) were systematically studied by performing ab initio calculations at the MP2(full)/6-31G(2df,p) level of theory...
August 11, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28795201/downstream-processing-technologies-capturing-and-final-purification-opportunities-for-innovation-change-and-improvement-a-review-of-downstream-processing-developments-in-protein-purification
#16
Nripen Singh, Sibylle Herzer
Increased pressure on upstream processes to maximize productivity has been crowned with great success, although at the cost of shifting the bottleneck to purification. As drivers were economical, focus is on now on debottlenecking downstream processes as the main drivers of high manufacturing cost. Devising a holistically efficient and economical process remains a key challenge. Traditional and emerging protein purification strategies with particular emphasis on methodologies implemented for the production of recombinant proteins of biopharmaceutical importance are reviewed...
August 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28746418/a-user-friendly-low-cost-turbidostat-with-versatile-growth-rate-estimation-based-on-an-extended-kalman-filter
#17
Stefan A Hoffmann, Christian Wohltat, Kristian M Müller, Katja M Arndt
For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization...
2017: PloS One
https://www.readbyqxmd.com/read/28746335/adjudicating-between-face-coding-models-with-individual-face-fmri-responses
#18
Johan D Carlin, Nikolaus Kriegeskorte
The perceptual representation of individual faces is often explained with reference to a norm-based face space. In such spaces, individuals are encoded as vectors where identity is primarily conveyed by direction and distinctiveness by eccentricity. Here we measured human fMRI responses and psychophysical similarity judgments of individual face exemplars, which were generated as realistic 3D animations using a computer-graphics model. We developed and evaluated multiple neurobiologically plausible computational models, each of which predicts a representational distance matrix and a regional-mean activation profile for 24 face stimuli...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28730360/characterization-of-extracellular-polymeric-substance-eps-fractions-produced-by-microcystis-aeruginosa-under-the-stress-of-linoleic-acid-sustained-release-microspheres
#19
Lixiao Ni, Danye Li, Shiyi Rong, Lili Su, Wei Zhou, Peifang Wang, Chao Wang, Shiyin Li, Kumud Acharya
This paper focuses on the characterization of extracellular polymeric substances (EPS), which are composed of soluble EPS (SL-EPS), loosely bound EPS (LB-EPS), and tightly bound EPS (TB-EPS) produced by Microcystis aeruginosa under the stress of linoleic acid (LA) and LA sustained-release microspheres. Three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy and Fourier transform infrared (FTIR) spectrometry were used to characterize three forms of EPS while the content of polysaccharide and protein was tested, respectively...
July 20, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28730305/self-assembly-of-the-polymer-brush-grafted-silica-colloidal%C3%A2-array-for-recognition-of-proteins
#20
Wei Chen, Kenneth J Shea, Min Xue, Lili Qiu, Yunhe Lan, Zihui Meng
Three-dimensional photonic crystal sensors are attractive platforms for autonomous chemical sensing and colorimetric bioassays. At present, the photonic crystal sensors with inverse opal structure were extensively studied, which swells or shrinks in response to the analytes. However, the fabrication of inverse opal sensors still remains a major challenge. Herein, we propose a simple and versatile approach to fabricate 3D opal photonic sensors. This photonic crystal is fabricated via assembly of monodispersed silica particles grafted with linear polymeric ligands (SiO2@LPs)...
July 20, 2017: Analytical and Bioanalytical Chemistry
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