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https://www.readbyqxmd.com/read/28735414/bone-mechanobiology-in-mice-toward-single-cell-in-vivo-mechanomics
#1
Ariane Scheuren, Esther Wehrle, Felicitas Flohr, Ralph Müller
Mechanically driven bone (re)modeling is a multiscale process mediated through complex interactions between multiple cell types and their microenvironments. However, the underlying mechanisms of how cells respond to mechanical signals are still unclear and are at the focus of the field of bone mechanobiology. Traditionally, this complex process has been addressed by reducing the system to single scales and cell types. It is only recently that more integrative approaches have been established to study bone mechanobiology across multiple scales in which mechanical load at the organ level is related to molecular responses at the cellular level...
July 22, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28735107/integrative-modelling-of-cellular-assemblies
#2
REVIEW
Agnel Praveen Joseph, Guido Polles, Frank Alber, Maya Topf
A wide variety of experimental techniques can be used for understanding the precise molecular mechanisms underlying the activities of cellular assemblies. The inherent limitations of a single experimental technique often requires integration of data from complementary approaches to gain sufficient insights into the assembly structure and function. Here, we review popular computational approaches for integrative modelling of cellular assemblies, including protein complexes and genomic assemblies. We provide recent examples of integrative models generated for such assemblies by different experimental techniques, especially including data from 3D electron microscopy (3D-EM) and chromosome conformation capture experiments, respectively...
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28735040/co-encapsulation-of-paclitaxel-and-c6-ceramide-in-tributyrin-containing-nanocarriers-improve-co-localization-in-the-skin-and-potentiate-cytotoxic-effects-in-2d-and-3d-models
#3
Vanessa F M Carvalho, Amanda Migotto, Daniela V Giacone, Débora P de Lemos, Thalita B Zanoni, Silvya S Maria-Engler, Leticia V Costa-Lotufo, Luciana B Lopes
Considering that tumor development is generally multifactorial, therapy with a combination of agents capable of potentiating cytotoxic effects is promising. In this study, we co-encapsulated C6 ceramide (0.35%) and paclitaxel (0.50%) in micro and nanoemulsions containing tributyrin (a butyric acid pro-drug included for potentiation of cytotoxicity), and compared their ability to co-localize the drugs in viable skin layers. The nanoemulsion delivered 2- and 2.4-fold more paclitaxel into viable skin layers of porcine skin in vitro at 4 and 8h post-application than the microemulsion, and 1...
July 19, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28734609/reinforcements-in-avian-wing-bones-experiments-analysis-and-modeling
#4
E Novitskaya, C J Ruestes, M M Porter, V A Lubarda, M A Meyers, J McKittrick
Almost all species of modern birds are capable of flight; the mechanical competency of their wings and the rigidity of their skeletal system evolved to enable this outstanding feat. One of the most interesting examples of structural adaptation in birds is the internal structure of their wing bones. In flying birds, bones need to be sufficiently strong and stiff to withstand forces during takeoff, flight, and landing, with a minimum of weight. The cross-sectional morphology and presence of reinforcing structures (struts and ridges) found within bird wing bones vary from species to species, depending on how the wings are utilized...
July 14, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28734530/joint-optic-disc-and-cup-boundary-extraction-from-monocular-fundus-images
#5
Arunava Chakravarty, Jayanthi Sivaswamy
BACKGROUND AND OBJECTIVE: Accurate segmentation of optic disc and cup from monocular color fundus images plays a significant role in the screening and diagnosis of glaucoma. Though optic cup is characterized by the drop in depth from the disc boundary, most existing methods segment the two structures separately and rely only on color and vessel kink based cues due to the lack of explicit depth information in color fundus images. METHODS: We propose a novel boundary-based Conditional Random Field formulation that extracts both the optic disc and cup boundaries in a single optimization step...
August 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28734207/in-silico-designing-of-therapeutic-protein-enriched-with-branched-chain-amino-acids-for-the-dietary-treatment-of-chronic-liver-disease
#6
Sunil L, Prasanna Vasu
Leucine, isoleucine, and valine are three essential branched-chain amino acids (BCAA) account for 40-45% of total essential amino acids. BCAA stimulates protein synthesis primarily in skeletal muscles, and it can directly transport to circulatory blood stream bypassing the liver. Hence, a protein enriched with BCAA is an important therapeutic target for the dietary treatment of chronic liver disease. The present study is to design a synthetic protein enriched with BCAA and the challenge is to maximize the BCAA content, keeping the balanced ratio of leucine, isoleucine, valine - 2: 1: 1...
July 12, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28734076/ensemble-characterization-of-an-intrinsically-disordered-fg-nup-peptide-and-its-f-a-mutant-in-dmso-d6
#7
Korey M Reid, Punnepalli Sunanda, S Raghothama, V V Krishnan
Intrinsically disordered proteins (IDP) lack a well-defined 3D-structure under physiological conditions, yet, the inherent disorder represented by an ensemble of conformation plays a critical role in many cellular and regulatory processes. Nucleoporins, or Nups, are the proteins found in the nuclear pore complex (NPC). The central pore of the NPC is occupied by Nups, which have phenylalanine-glycine domain repeats and are intrinsically disordered, and therefore are termed FG-Nups. These FG-domain repeats exhibit differing cohesiveness character and differ from least (FG) to most (GLFG) cohesive...
July 22, 2017: Biopolymers
https://www.readbyqxmd.com/read/28734017/evaluation-of-the-impact-of-strain-correction-on-the-orientation-of-cardiac-diffusion-tensors-with-in-vivo-and-ex-vivo-porcine-hearts
#8
Pedro F Ferreira, Sonia Nielles-Vallespin, Andrew D Scott, Ranil de Silva, Philip J Kilner, Daniel B Ennis, Daniel A Auger, Jonathan D Suever, Xiaodong Zhong, Bruce S Spottiswoode, Dudley J Pennell, Andrew E Arai, David N Firmin
PURPOSE: To evaluate the importance of strain-correcting stimulated echo acquisition mode echo-planar imaging cardiac diffusion tensor imaging. METHODS: Healthy pigs (n = 11) were successfully scanned with a 3D cine displacement-encoded imaging with stimulated echoes and a monopolar-stimulated echo-planar imaging diffusion tensor imaging sequence at 3 T during diastasis, peak systole, and strain sweet spots in a midventricular short-axis slice. The same diffusion tensor imaging sequence was repeated ex vivo after arresting the hearts in either a relaxed (KCl-induced) or contracted (BaCl2 -induced) state...
July 21, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28733975/deep-convolutional-neural-network-and-3d-deformable-approach-for-tissue-segmentation-in-musculoskeletal-magnetic-resonance-imaging
#9
Fang Liu, Zhaoye Zhou, Hyungseok Jang, Alexey Samsonov, Gengyan Zhao, Richard Kijowski
PURPOSE: To describe and evaluate a new fully automated musculoskeletal tissue segmentation method using deep convolutional neural network (CNN) and three-dimensional (3D) simplex deformable modeling to improve the accuracy and efficiency of cartilage and bone segmentation within the knee joint. METHODS: A fully automated segmentation pipeline was built by combining a semantic segmentation CNN and 3D simplex deformable modeling. A CNN technique called SegNet was applied as the core of the segmentation method to perform high resolution pixel-wise multi-class tissue classification...
July 21, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28733928/structural-neurodegeneration-correlates-with-early-diabetic-retinopathy
#10
Ulrik Frydkjaer-Olsen, Rasmus Soegaard Hansen, Tunde Peto, Jakob Grauslund
PURPOSE: To examine differences in structural and functional neurodegenerative measurements between patients with no and early diabetic retinopathy (DR). METHODS: In this cross-sectional study, we examined 103 patients with type 2 diabetes mellitus. In 7-field fundus photographs acquired with Topcon TRC-NW6S, a single, certified grader determined the presence of DR according to the Early Treatment Diabetic Retinopathy Study (ETDRS) scale. Retinal neurodegeneration was evaluated by Topcon 3D OCT-2000 spectral domain optical coherence tomography (OCT) and by a RETI-scan multifocal electroretinography (mf-ERG) system in rings 1-6...
July 21, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28733734/combined-in-vivo-and-ex-vivo-analysis-of-mesh-mechanics-in-a-porcine-hernia-model
#11
Lindsey G Kahan, Spencer P Lake, Jared M McAllister, Wen Hui Tan, Jennifer Yu, Dominic Thompson, L Michael Brunt, Jeffrey A Blatnik
BACKGROUND: Hernia meshes exhibit variability in mechanical properties, and their mechanical match to tissue has not been comprehensively studied. We used an innovative imaging model of in vivo strain tracking and ex vivo mechanical analysis to assess effects of mesh properties on repaired abdominal walls in a porcine model. We hypothesized that meshes with dissimilar mechanical properties compared to native tissue would alter abdominal wall mechanics more than better-matched meshes. METHODS: Seven mini-pigs underwent ventral hernia creation and subsequent open repair with one of two heavyweight polypropylene meshes...
July 21, 2017: Surgical Endoscopy
https://www.readbyqxmd.com/read/28733649/an-in-vitro-model-for-the-ocular-surface-and-tear-film-system
#12
Qiaozhi Lu, Hongbo Yin, Michael P Grant, Jennifer H Elisseeff
Dry eye is a complicated ocular surface disease whose exact pathogenesis is not yet fully understood. For the therapeutic evaluation and pathogenesis study of dry eye, we established an in vitro three-dimensional (3D) coculture model for the ocular surface. It is composed of rabbit conjunctival epithelium and lacrimal gland cell spheroids, and recapitulates the aqueous and mucin layers of the tear film. We first investigated the culture conditions for both cell types to optimize their secretory functions, by employing goblet cell enrichment, air-lifting culture, and 3D spheroid formation techniques...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733616/capturing-3d-water-flow-in-rooted-soil-by-ultra-fast-neutron-tomography
#13
Christian Tötzke, Nikolay Kardjilov, Ingo Manke, Sascha E Oswald
Water infiltration in soil is not only affected by the inherent heterogeneities of soil, but even more by the interaction with plant roots and their water uptake. Neutron tomography is a unique non-invasive 3D tool to visualize plant root systems together with the soil water distribution in situ. So far, acquisition times in the range of hours have been the major limitation for imaging 3D water dynamics. Implementing an alternative acquisition procedure we boosted the speed of acquisition capturing an entire tomogram within 10 s...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733223/sequencing-of-fic1-bsep-and-mdr3-in-a-large-cohort-of-patients-with-cholestasis-revealed-a-high-number-of-different-genetic-variants
#14
Carola Dröge, Michele Bonus, Ulrich Baumann, Caroline Klindt, Elke Lainka, Simone Kathemann, Florian Brinkert, Enke Grabhorn, Eva-Doreen Pfister, Daniel Wenning, Alexander Fichtner, Daniel N Gotthardt, Karl Heinz Weiss, Patrick McKiernan, Ratna Dua Puri, I C Verma, Stefanie Kluge, Holger Gohlke, Lutz Schmitt, Ralf Kubitz, Dieter Häussinger, Verena Keitel
BACKGROUND&AIMS: The bile salt export pump (BSEP, ABCB11), multidrug resistance protein 3 (MDR3, ABCB4) and the ATPase familial intrahepatic cholestasis 1 (FIC1, ATP8B1) mediate bile formation. Mutations in these genes underlie cholestatic liver diseases ranging from intrahepatic cholestasis of pregnancy, benign recurrent intrahepatic cholestasis or low phospholipid-associated cholelithiasis to progressive familial intrahepatic cholestasis. METHODS: Coding exons with flanking intron regions of ATP8B1, ABCB11, and ABCB4 were sequenced in cholestatic patients with assumed genetic cause...
July 18, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28732246/inspiration-from-heart-development-biomimetic-development-of-functional-human-cardiac-organoids
#15
Dylan J Richards, Robert C Coyle, Yu Tan, Jia Jia, Kerri Wong, Katelynn Toomer, Donald R Menick, Ying Mei
Recent progress in human organoids has provided 3D tissue systems to model human development, diseases, as well as develop cell delivery systems for regenerative therapies. While direct differentiation of human embryoid bodies holds great promise for cardiac organoid production, intramyocardial cell organization during heart development provides biological foundation to fabricate human cardiac organoids with defined cell types. Inspired by the intramyocardial organization events in coronary vasculogenesis, where a diverse, yet defined, mixture of cardiac cell types self-organizes into functional myocardium in the absence of blood flow, we have developed a defined method to produce scaffold-free human cardiac organoids that structurally and functionally resembled the lumenized vascular network in the developing myocardium, supported hiPSC-CM development and possessed fundamental cardiac tissue-level functions...
July 12, 2017: Biomaterials
https://www.readbyqxmd.com/read/28732174/spatial-organization-of-fibroblast-and-spermatocyte-nuclei-with-different-b-chromosome-content-in-korean-field-mouse-i-apodemus-peninsulae-i-rodentia-muridae
#16
Tatyana V Karamysheva, Anna A Torgasheva, Yaroslav R Yefremov, Anton G Bogomolov, Thomas Liehr, Pavel M Borodin, Nikolay B Rubtsov
Korean field mouse (<i>Apodemus peninsulae</i>) shows a wide variation in the number of B chromosomes composed of constitutive heterochromatin. For this reason, it provides a good model to study the influence of the number of centromeres and amount of heterochromatin on spatial organization of interphase nuclei. We analyzed the three-dimensional organization of fibroblast and spermatocyte nuclei of the field mice carrying different number of B chromosomes using laser scanning microscopy and 3D fluorescence <i>in situ</i> hybridization...
July 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28732052/protein-asparagine-deamidation-prediction-based-on-structures-with-machine-learning-methods
#17
Lei Jia, Yaxiong Sun
Chemical stability is a major concern in the development of protein therapeutics due to its impact on both efficacy and safety. Protein "hotspots" are amino acid residues that are subject to various chemical modifications, including deamidation, isomerization, glycosylation, oxidation etc. A more accurate prediction method for potential hotspot residues would allow their elimination or reduction as early as possible in the drug discovery process. In this work, we focus on prediction models for asparagine (Asn) deamidation...
2017: PloS One
https://www.readbyqxmd.com/read/28731812/3d-printed-visceral-aneurysm-models-based-on-ct-data-for-simulations-of-endovascular-embolization-evaluation-of-size-and-shape-accuracy
#18
Eisuke Shibata, Hidemasa Takao, Shiori Amemiya, Kuni Ohtomo
OBJECTIVE: The objective of this study is to verify the accuracy of 3D-printed hollow models of visceral aneurysms created from CT angiography (CTA) data, by evaluating the sizes and shapes of aneurysms and related arteries. SUBJECTS AND METHODS: From March 2006 to August 2015, 19 true visceral aneurysms were embolized via interventional radiologic treatment provided by the radiology department at our institution; aneurysms with bleeding (n = 3) or without thin-slice (< 1 mm) preembolization CT data (n = 1) were excluded...
August 2017: AJR. American Journal of Roentgenology
https://www.readbyqxmd.com/read/28731499/the-frontal-sinus-cavity-exhibits-sexual-dimorphism-in-3d-cone-beam-ct-images-and-can-be-used-for-sex-determination
#19
Isabela G G Choi, Eduardo F Duailibi-Neto, Thiago L Beaini, Renan L B da Silva, Israel Chilvarquer
Few studies have assessed the use of the frontal sinus cavities for sex differentiation. In this study, a new methodology was used to assess the reliability of CBCT images of the frontal sinus cavity for determining sex based on the sexual dimorphism found in this anatomical structure. The survey sample consisted of 130 scans that were reconstructed three-dimensionally. 3D images of the cavity volume in the frontal, lateral, and basal views were exported in TIFF. The following variables were measured in a second program: area, perimeter, bounding rectangle, ellipse fit, circularity, aspect ratio, roundness, solidity, and Feret's diameter...
July 21, 2017: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/28731328/bisphosphonate-functionalized-hydroxyapatite-nanoparticles-for-the-delivery-of-the-bromodomain-inhibitor-jq1-in-the-treatment-of-osteosarcoma
#20
Victoria Wu, Jarrett Mickens, Vuk Uskokovic
Osteosarcoma (OS) is one of the most common neoplasia among children and its survival statistics have been stagnating since the combinatorial anticancer therapy triad was first introduced. Here we report on the assessment of the effect of hydroxyapatite (HAp) nanoparticles loaded with medronate, the simplest bisphosphonate, as a bone-targeting agent and JQ1, a small-molecule bromodomain inhibitor, as a chemotherapeutic in different 2D and 3D K7M2 OS in vitro models. Both additives decreased the crystallinity of HAp, but the effect was more intense for medronate because of its higher affinity for HAp...
July 21, 2017: ACS Applied Materials & Interfaces
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