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https://www.readbyqxmd.com/read/27914354/3d-qsar-predictions-for-%C3%AE-cyclodextrin-binding-constants-using-quantum-mechanically-based-descriptors
#1
Lukas Linden, Kai-Uwe Goss, Satoshi Endo
Binding of organic chemicals to α-cyclodextrin (αCD) is a typical example for host-guest complexation that is influenced by the 3D-structure of both the binding site (host) and the solute (guest). Prediction of the binding constant is challenging and requires a successful representation of the binding site-solute interactions in the 3D-space. In this study, we tested if a 3D quantitative structure activity relationship (3D-QSAR) model with quantum mechanically based local sigma profiles (LSPs) derived from the COSMOsar3D method is capable of predicting αCD binding constants from the most recent literature and how the model performs in comparison to a standard comparative molecular field analysis and to a reference 2D-QSAR...
November 30, 2016: Chemosphere
https://www.readbyqxmd.com/read/27914271/individual-exposure-estimates-may-be-erroneous-when-spatiotemporal-variability-of-air-pollution-and-human-mobility-are-ignored
#2
Yoo Min Park, Mei-Po Kwan
This study aims to empirically demonstrate the necessity to consider both the spatiotemporal variability of air pollution and individual daily movement patterns in exposure and health risk assessment. It compares four different types of exposure estimates generated by using (1) individual movement data and hourly air pollution concentrations; (2) individual movement data and daily average air pollution data; (3) residential location and hourly pollution levels; and (4) residential location and daily average pollution data...
November 30, 2016: Health & Place
https://www.readbyqxmd.com/read/27914265/automated-quantification-of-three-dimensional-organization-of-fiber-like-structures-in-biological-tissues
#3
Zhiyi Liu, Dimitra Pouli, Disha Sood, Aswin Sundarakrishnan, Carrie K Hui Mingalone, Lisa M Arendt, Carlo Alonzo, Kyle P Quinn, Charlotte Kuperwasser, Li Zeng, Thomas Schnelldorfer, David L Kaplan, Irene Georgakoudi
Fiber-like structures are prevalent in biological tissues, yet quantitative approaches to assess their three-dimensional (3D) organization are lacking. We develop 3D directional variance, as a quantitative biomarker of truly 3D fibrillar organization by extending the directional statistics formalism developed for describing circular data distributions (i.e. when 0° and 360° are equivalent) to axial ones (i.e. when 0° and 180° are equivalent). Significant advantages of this analysis include its time efficiency, sensitivity and ability to provide quantitative readouts of organization over different size scales of a given data set...
November 25, 2016: Biomaterials
https://www.readbyqxmd.com/read/27914061/probing-oligomerized-conformations-of-defensin-in-the-membrane
#4
Wenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, Ruth Nussinov
Computational prediction and design of membrane protein-protein interactions facilitate biomedical engineering and biotechnological applications. Due to their antimicrobial activity, human defensins play an important role in the innate immune system. Human defensins are attractive pharmaceutical targets due to their small size, broad activity spectrum, reduced immunogenicity, and resistance to proteolysis. Protein engineering based modification of defensins can improve their pharmaceutical properties. Here we present an approach to computationally probe defensins' oligomerization states in the membrane...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914060/a-protocol-for-the-design-of-protein-and-peptide-nanostructure-self-assemblies-exploiting-synthetic-amino-acids
#5
Nurit Haspel, Jie Zheng, Carlos Aleman, David Zanuy, Ruth Nussinov
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#6
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914004/hybrid-receptor-bound-mm-gbsa-per-residue-energy-based-pharmacophore-modelling-enhanced-approach-for-identification-of-selective-lta4h-inhibitors-as-potential-anti-inflammatory-drugs
#7
Patrick Appiah-Kubi, Mahmoud Soliman
Leukotriene A4 hydrolase has been identified as an enzyme with dual anti- and pro-inflammatory role, thus, the conversion of leukotriene to leukotriene B4 in the initiation stage of inflammation and the removal of the chemotactic Pro-Gly-Pro tripeptide. These findings make leukotriene A4 hydrolase an attractive drug target: suggesting an innovative approach towards the identification and design of novel class of compounds that can selectively inhibit leukotriene B4 synthesis while sparing the aminopeptidase activity...
December 2, 2016: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/27913958/the-effect-of-mass-transfer-parameterization-and-ice-retention-on-the-scavenging-and-redistribution-of-so2-by-a-deep-convective-cloud
#8
Vladan Vučković, Dragana Vujović
A chemistry module with the aqueous chemistry coupled with the complex 3D nonhydrostatic atmospheric model is used to investigate how the representation of gas-aqueous mass transfer and ice retention affect the SO2 redistribution in the presence of a convective cloud. Gas uptake to the liquid water is calculated using both Henry's law equilibrium (HE) and kinetic mass transport (KMT). The constant retention coefficients for SO2 (k ret = 0.46) and for H2O2 (k ret = 0.64) are used. It is shown that the amount of SO2 in the air at higher altitudes (10-12 km) is greater when partial retention (PR) is included...
December 2, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27913951/stereolithography-based-3d-printed-pillar-plates-that-minimizes-fluid-transfers-during-enzyme-linked-immunosorbent-assays
#9
Justin D McCallen, Alison Schaefer, Phoebe Lee, Loretta Hing, Samuel K Lai
Enzyme linked immunosorbent assay (ELISA) is one of the most popular and indispensable tools in molecular biology. Despite numerous advances in ELISA methods that markedly improve the sensitivity and throughput of detection, a hallmark of all ELISA continues to be repeated pipetting of fluids that is not only cumbersome but can easily introduce errors or contaminations. Robotics, despite obvious advantages, remains expensive. Here, we designed and produced cheap "pillar plates" using stereolithography-based 3D printing that can be readily inserted into conventional 96- and 384- well plates and serve as the substrate for ELISA...
December 2, 2016: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/27913902/a-new-multiscale-micromechanical-model-of-vertebral-trabecular-bones
#10
Rami Haj-Ali, Eyass Massarwa, Jacob Aboudi, Fabio Galbusera, Uwe Wolfram, Hans-Joachim Wilke
A new three-dimensional (3D) multiscale micromechanical model has been suggested as adept at predicting the overall linear anisotropic mechanical properties of a vertebral trabecular bone (VTB) highly porous microstructure. A nested 3D modeling analysis framework spanning the multiscale nature of the VTB is presented herein. This hierarchical analysis framework employs the following micromechanical methods: the 3D parametric high-fidelity generalized method of cells (HFGMC) as well as the 3D sublaminate model...
December 2, 2016: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/27913901/3d-active-passive-response-of-human-knee-joint-in-gait-is-markedly-altered-when-simulated-as-a-planar-2d-joint
#11
H Marouane, A Shirazi-Adl, M Adouni
Musculoskeletal models of the lower extremity make a number of important assumptions when attempting to estimate muscle forces and tibiofemoral compartmental loads in activities such as gait. The knee is commonly idealized as a planar 2D joint in the sagittal plane with no consideration of motions and equilibrium in remaining planes. With muscle forces predicted, the static equilibrium in the frontal plane is then used to estimate compartmental loads neglecting also joint passive resistance and assuming condylar contact centers...
December 2, 2016: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/27913880/forensic-3d-documentation-of-skin-injuries
#12
Chiara Villa
An accurate and precise documentation of injuries is fundamental in a forensic pathological context. Photographs and manual measurements are taken of all injuries during autopsies, but ordinary photography projects a 3D wound on a 2D space. Using technologies such as photogrammetry, it is possible to create 3D detailed, to-scale, true-color documentation of skin injuries from 2D pictures. A comparison between the measurements of 165 lesions taken during autopsies and on photogrammetrically processed pictures was performed...
December 2, 2016: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/27913755/applications-of-three-dimensional-printing-in-surgery
#13
REVIEW
Chi Li, Tsz Fung Cheung, Vei Chen Fan, Kin Man Sin, Chrisity Wai Yan Wong, Gilberto Ka Kit Leung
Three-dimensional (3D) printing is a rapidly advancing technology in the field of surgery. This article reviews its contemporary applications in 3 aspects of surgery, namely, surgical planning, implants and prostheses, and education and training. Three-dimensional printing technology can contribute to surgical planning by depicting precise personalized anatomy and thus a potential improvement in surgical outcome. For implants and prosthesis, the technology might overcome the limitations of conventional methods such as visual discrepancy from the recipient's body and unmatching anatomy...
December 2, 2016: Surgical Innovation
https://www.readbyqxmd.com/read/27913679/modelling-gtpase-dynamics-to-understand-rhoa-driven-cancer-cell-invasion
#14
REVIEW
Joseph H R Hetmanski, Jean-Marc Schwartz, Patrick T Caswell
Metastasis, initially driven by cells migrating and invading through the local environment, leads to most cancer-associated deaths. Cells can use a variety of modes to move in vitro, all of which depend on Rho GTPases at some level. While traditionally it was thought that Rac1 activity drives protrusive lamellipodia at the leading edge of a polarised cell while RhoA drives rear retraction, more recent work in 3D microenvironments has revealed a much more complicated picture of GTPase dynamics. In particular, RhoA activity can dominate the leading edge polymerisation of actin to form filopodial actin-spike protrusions that drive more invasive cell migration...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913653/dimensional-evaluation-of-patient-specific-3d-printing-using-calcium-phosphate-cement-for-craniofacial-bone-reconstruction
#15
Liciane Sabadin Bertol, Rodrigo Schabbach, Luís Alberto Loureiro Dos Santos
The 3D printing process is highlighted nowadays as a possibility to generate individual parts with complex geometries. Moreover, the development of 3D printing hardware, software and parameters permits the manufacture of parts that can be not only used as prototypes, but are also made from materials that are suitable for implantation. In this way, this study investigates the process involved in the production of patient-specific craniofacial implants using calcium phosphate cement, and its dimensional accuracy...
December 1, 2016: Journal of Biomaterials Applications
https://www.readbyqxmd.com/read/27913424/digital-3d-reconstructions-using-histological-serial-sections-of-lung-tissue-including-the-alveolar-capillary-network
#16
Roman Grothausmann, Lars Knudsen, Matthias Ochs, Christian Mühlfeld
The alveolar capillary network (ACN) provides an enormously large surface area that is necessary for pulmonary gas exchange. Changes of the ACN during normal or pathological development or in pulmonary diseases are of great functional impact and warrant further analysis. Due to the complexity of the three-dimensional (3D) architecture of the ACN, 2D approaches are limited in providing a comprehensive impression of the characteristics of the normal ACN or the nature of its alterations. Stereological methods offer a quantitative way to assess the ACN in 3D in terms of capillary volume, surface area or number but lack a 3D visualization to interpret the data...
December 2, 2016: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/27913340/efficient-3d-reconstruction-in-ultrasound-elastography-via-a-sparse-iteration-based-on-markov-random-fields
#17
Atul Ingle, Tomy Varghese, William Sethares
Percutaneous needle-based liver ablation procedures are becoming increasingly common for treatment of small isolated tumors in hepatocellular carcinoma patients who are not candidates for surgery. Rapid three dimensional visualization of liver ablations has potential clinical value because it can enable interventional radiologists to plan and execute needle-based ablation procedures with real time feedback. Ensuring the right volume of tissue is ablated is desirable to avoid recurrence of tumors from residual untreated cancerous cells...
November 29, 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/27913318/walsh-hadamard-based-3d-steganography-for-protecting-sensitive-information-in-point-of-care
#18
Alsharif Abuadbba, Ibrahim Khalil
Remote points-of-care has recently had a lot of attention for their advantages such as saving lives and cost reduction. The transmitted streams usually contain (1) normal biomedical signals (e.g. ECG) and (2) highly private information (e.g. patient identity). Despite the obvious advantages, the primary concerns are privacy and authenticity of the transferred data. Therefore, this paper introduces a novel steganographic mechanism that ensures (1) strong privacy preservation of private information by random concealing inside the transferred signals employing a key, and (2) evidence of originality for the biomedical signals...
November 29, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27913249/comparison-of-the-transcriptomic-profile-of-hepatic-human-induced-pluripotent-stem-like-cells-cultured-in-plates-and-in-a-3d-microscale-dynamic-environment
#19
Eric Leclerc, Keiichi Kimura, Marie Shinohara, Mathieu Danoy, Morgane Le Gall, Taketomo Kido, Atsushi Miyajima, Teruo Fujii, Yasuyuki Sakai
We have compared the transcriptomic profiles of human induced pluripotent stem cells after their differentiation in hepatocytes like cells in plates and microfluidic biochips. The biochips provided a 3D and dynamic support during the cell differentiation when compared to the 2D static cultures in plates. The microarray have demonstrated the up regulation of important pathway related to liver development and maturation during the culture in biochips. Furthermore, the results of the transcriptomic profile, coupled with immunostaining, and RTqPCR analysis have shown typical biomarkers illustrating the presence of responders of biliary like cells, hepatocytes like cells, and endothelial like cells...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27913222/human-liver-regeneration-in-advanced-cirrhosis-is-organized-by-the-portal-tree
#20
Katalin Dezső, András Rókusz, Edina Bugyik, Armanda Szücs, András Szuák, Bence Dorogi, Mátyás Kiss, Ágnes Nemeskéri, Péter Nagy, Sándor Paku
BACKGROUND&AIMS: In advanced cirrhosis new hepatocytic nodules are generated by budding of ductules in areas of parenchymal extinction. However, the vascular alterations in the areas of parenchymal extinction, the blood supply and the structure of the new hepatocytic nodules have not been analyzed in detail. METHODS: Explanted human cirrhotic livers of three different etiologies and two experimental models of cirrhosis in rats were examined thoroughly. 3D reconstruction of the immunohistochemically stained serial sections and casting of human and experimental cirrhotic livers have been used to reveal the structural organization of the regenerative buds...
November 29, 2016: Journal of Hepatology
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