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https://www.readbyqxmd.com/read/29233747/structural-changes-of-homodimers-in-the-pdb
#1
Ryotaro Koike, Takayuki Amemiya, Tatsuya Horii, Motonori Ota
Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes and magnitude from the two structural complexes with the same binding mode...
December 9, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29232186/cemented-or-cementless-total-knee-arthroplasty-comparative-results-of-200-cases-at-a-minimum-follow-up-of-11-years
#2
Jean-Louis Prudhon, Régis Verdier
INTRODUCTION: Since 1996 we have been using cementless fixation with hydroxyapatite (HA) coating. The purpose of this paper is to compare survivorship of a series of 100 cemented Total Knee Arthroplasty (TKA) to a similar series of 100 cementless with a follow up of 11-16 years. Material methods: Both TKA are mobile bearing total knee postero-stabilized. They can be used with cement or without cement. Among 1030 New Wave TKATM implanted from 2002 to 2015 we have identified 100 cemented TKAs and 100 cementless TKAs...
2017: SICOT-J
https://www.readbyqxmd.com/read/29231177/hindrances-to-precise-recovery-of-cellular-forces-in-fibrous-biopolymer-networks
#3
Yunsong Zhang, Jingchen Feng, Shay I Heizler, Herbert Levine
How cells move through the three-dimensional extracellular matrix (ECM) is of increasing interest in attempts to understand important biological processes such as cancer metastasis. Just as in motion on flat surfaces, it is expected that experimental measurements of cell-generated forces will provide valuable information for uncovering the mechanisms of cell migration. However, the recovery of forces in fibrous biopolymer networks may suffer from large errors. Here, within the framework of lattice-based models, we explore possible issues in force recovery by solving the inverse problem: how can one determine the forces cells exert to their surroundings from the deformation of the ECM? Our results indicate that irregular cell traction patterns, the uncertainty of local fiber stiffness, the non-affine nature of ECM deformations and inadequate knowledge of network topology will all prevent the precise force determination...
December 12, 2017: Physical Biology
https://www.readbyqxmd.com/read/29227618/tackling-the-challenges-of-dynamic-experiments-using-liquid-cell-transmission-electron-microscopy
#4
Lucas R Parent, Evangelos Bakalis, Maria Proetto, Yiwen Li, Chiwoo Park, Francesco Zerbetto, Nathan C Gianneschi
Revolutions in science and engineering frequently result from the development, and wide adoption, of a new, powerful characterization or imaging technique. Beginning with the first glass lenses and telescopes in astronomy, to the development of visual-light microscopy, staining techniques, confocal microscopy, and fluorescence super-resolution microscopy in biology, and most recently aberration-corrected, cryogenic, and ultrafast (4D) electron microscopy, X-ray microscopy, and scanning probe microscopy in nanoscience...
December 11, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29227492/impact-of-complex-surfaces-on-biomicrorheological-measurements-using-optical-tweezers
#5
Shu Zhang, Lachlan J Gibson, Alexander B Stilgoe, Timo A Nieminen, Halina Rubinsztein-Dunlop
The characterisation of physical properties in biologically relevant processes and the development of novel microfluidic devices for this purpose are experiencing a great resurgence at present. In many of measurements of this type where a probe in a fluid is used, the strong influence of the boundaries of the volume used is a serious problem. In these geometries the proximity of a probe to a wall can severely influence the measurement. However, although much knowledge has been gained about flat walls, to date, the effect of non-planar surfaces at microscopic scale on rotational motion of micro-objects has not been studied...
December 11, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/29225692/recent-advances-in-radiation-oncology
#6
REVIEW
Cristina Garibaldi, Barbara Alicja Jereczek-Fossa, Giulia Marvaso, Samantha Dicuonzo, Damaris Patricia Rojas, Federica Cattani, Anna Starzyńska, Delia Ciardo, Alessia Surgo, Maria Cristina Leonardi, Rosalinda Ricotti
Radiotherapy (RT) is very much a technology-driven treatment modality in the management of cancer. RT techniques have changed significantly over the past few decades, thanks to improvements in engineering and computing. We aim to highlight the recent developments in radiation oncology, focusing on the technological and biological advances. We will present state-of-the-art treatment techniques, employing photon beams, such as intensity-modulated RT, volumetric-modulated arc therapy, stereotactic body RT and adaptive RT, which make possible a highly tailored dose distribution with maximum normal tissue sparing...
2017: Ecancermedicalscience
https://www.readbyqxmd.com/read/29225508/theory-of-energy-harvesting-from-heartbeat-including-the-effects-of-pleural-cavity-and-respiration
#7
Yangyang Zhang, Bingwei Lu, Chaofeng Lü, Xue Feng
Self-powered implantable devices with flexible energy harvesters are of significant interest due to their potential to solve the problem of limited battery life and surgical replacement. The flexible electronic devices made of piezoelectric materials have been employed to harvest energy from the motion of biological organs. Experimental measurements show that the output voltage of the device mounted on porcine left ventricle in chest closed environment decreases significantly compared to the case of chest open...
November 2017: Proceedings. Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29220402/bodily-motion-fluctuation-improves-reaching-success-rate-in-a-neurophysical-agent-via-geometric-stochastic-resonance
#8
Shogo Yonekura, Yasuo Kuniyoshi
Organisms generate a variety of noise types, including neural noise, sensory noise, and noise resulting from fluctuations associated with movement. Sensory and neural noises are known to induce stochastic resonance (SR), which improves information transfer to the subjects control systems, including the brain. As a consequence, sensory and neural noise provide behavioral benefits, such as stabilization of posture and enhancement of feeding efficiency. In contrast, the benefits of fluctuations in the movements of a biological system remain largely unclear...
2017: PloS One
https://www.readbyqxmd.com/read/29218871/extracting-a-biologically-relevant-latent-space-from-cancer-transcriptomes-with-variational-autoencoders
#9
Gregory P Way, Casey S Greene
The Cancer Genome Atlas (TCGA) has profiled over 10,000 tumors across 33 different cancer-types for many genomic features, including gene expression levels. Gene expression measurements capture substantial information about the state of each tumor. Certain classes of deep neural network models are capable of learning a meaningful latent space. Such a latent space could be used to explore and generate hypothetical gene expression profiles under various types of molecular and genetic perturbation. For example, one might wish to use such a model to predict a tumor's response to specific therapies or to characterize complex gene expression activations existing in differential proportions in different tumors...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29212760/large-scale-molecular-dynamics-simulation-of-coupled-dynamics-of-flow-and-glycocalyx-towards-understanding-atomic-events-on-an-endothelial-cell-surface
#10
Xi Zhuo Jiang, Haipeng Gong, Kai Hong Luo, Yiannis Ventikos
The glycocalyx has a prominent role in orchestrating multiple biological processes occurring at the plasma membrane. In this paper, an all-atom flow/glycocalyx system is constructed with the bulk flow velocity in the physiologically relevant ranges for the first time. The system is simulated by molecular dynamics using 5.8 million atoms. Flow dynamics and statistics in the presence of the glycocalyx are presented and discussed. Complex dynamic behaviours of the glycocalyx, particularly the sugar chains, are observed in response to blood flow...
December 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29212682/stable-migration-of-peri-apatite-coated-uncemented-tibial-components-in-a-multicentre-study
#11
M J Dunbar, E K Laende, D Collopy, C G Richardson
AIMS: Hydroxyapatite coatings for uncemented fixation in total knee arthroplasty can theoretically provide a long-lasting biological interface with the host bone. The objective of this study was to test this hypothesis with propriety hydroxyapatite, peri-apatite, coated tibial components using component migration measured with radiostereometric analysis over two years as an indicator of long-term fixation. PATIENTS AND METHODS: A total of 29 patients at two centres received uncemented PA-coated tibial components and were followed for two years with radiostereometric analysis exams to quantify the migration of the component...
December 2017: Bone & Joint Journal
https://www.readbyqxmd.com/read/29212004/investigating-focal-adhesion-substructures-by-localization-microscopy
#12
Hendrik Deschout, Ilia Platzman, Daniel Sage, Lely Feletti, Joachim P Spatz, Aleksandra Radenovic
Cells rely on focal adhesions (FAs) to carry out a variety of important tasks, including motion, environmental sensing, and adhesion to the extracellular matrix. Although attaining a fundamental characterization of FAs is a compelling goal, their extensive complexity and small size, which can be below the diffraction limit, have hindered a full understanding. In this study we have used single-molecule localization microscopy (SMLM) to investigate integrin β3 and paxillin in rat embryonic fibroblasts growing on two different extracellular matrix-representing substrates (i...
December 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29209065/cellular-automaton-models-for-time-correlated-random-walks-derivation-and-analysis
#13
J M Nava-Sedeño, H Hatzikirou, R Klages, A Deutsch
Many diffusion processes in nature and society were found to be anomalous, in the sense of being fundamentally different from conventional Brownian motion. An important example is the migration of biological cells, which exhibits non-trivial temporal decay of velocity autocorrelation functions. This means that the corresponding dynamics is characterized by memory effects that slowly decay in time. Motivated by this we construct non-Markovian lattice-gas cellular automata models for moving agents with memory...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29206189/vision-system-for-coarsely-estimating-motion-parameters-for-unknown-fast-moving-objects-in-space
#14
Min Chen, Koichi Hashimoto
Motivated by biological interests in analyzing navigation behaviors of flying animals, we attempt to build a system measuring their motion states. To do this, in this paper, we build a vision system to detect unknown fast moving objects within a given space, calculating their motion parameters represented by positions and poses. We proposed a novel method to detect reliable interest points from images of moving objects, which can be hardly detected by general purpose interest point detectors. 3D points reconstructed using these interest points are then grouped and maintained for detected objects, according to a careful schedule, considering appearance and perspective changes...
December 5, 2017: Sensors
https://www.readbyqxmd.com/read/29201303/bridging-graft-in-irreparable-massive-rotator-cuff-tears-autogenic-biceps-graft-versus-allogenic-dermal-patch-graft
#15
Sung Min Rhee, Joo Han Oh
Background: Few comparative studies have reported on the use of biologic grafts for irreparable massive rotator cuff tears. The purpose of this study was to assess the results of arthroscopic bridging graft in irreparable massive rotator cuff tears using an autogenic long head of biceps tendon (LHBT) or an allogenic dermal patch (ADP). Methods: We retrospectively reviewed 24 patients treated using the LHBT (group I) and eight patients with complete rupture of the LHBT treated using an ADP (group II) since 2011...
December 2017: Clinics in Orthopedic Surgery
https://www.readbyqxmd.com/read/29192498/membrane-protein-structure-in-live-cells-methodology-for-studying-drug-interaction-by-mass-spectrometry-based-footprinting
#16
Guo-Min Shen, Shuang Li, Weidong Cui, Shixuan Liu, Yihu Yang, Michael L Gross, Weikai Li
Mass spectrometry (MS) based footprinting is an emerging approach to study protein structure. Because integral membrane proteins are difficult targets for conventional structural biology, we recently developed a MS footprinting method to probe membrane protein/drug interactions in live cells. This method can detect structural difference between apo and drug-bound states of membrane proteins, with the changes inferred from MS quantification of the cysteine modification pattern, generated by residue-specific chemical labeling...
December 1, 2017: Biochemistry
https://www.readbyqxmd.com/read/29191861/determining-forward-speed-from-accelerometer-jiggle-in-aquatic-environments
#17
David E Cade, Kelly R Barr, John Calambokidis, Ari S Friedlaender, Jeremy A Goldbogen
How fast animals move is critical to understanding their energetic requirements, locomotor capacity, and foraging performance, yet current methods for measuring speed via animal-attached devices are not universally applicable. Here we present and evaluate a new method that relates forward speed to the stochastic motion of biologging devices since tag jiggle, the amplitude of the tag vibrations as measured by high sample rate accelerometers, increases exponentially with increasing speed. We successfully tested this method in a flow tank using two types of biologging devices and tested the method in situ on wild cetaceans spanning ∼3 to >20 m in length using two types of suction cup-attached and two types of dart-attached tag...
November 30, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29189331/ablative-radiotherapy-doses-for-locally-advanced-pancreatic-cancer-lapc
#18
Christopher H Crane, Eileen M O'Reilly
Standard palliative doses of radiation for locally advanced unresectable pancreatic cancer have had minimal to no impact on survival. Randomized trials evaluating these palliative doses have not shown a significant survival benefit with the use of radiation as consolidation after chemotherapy. Results from nonrandomized studies of 3- to 5-fraction low-dose stereotactic radiation (SBRT) have likewise had a minimal impact, but with less toxicity and a shorter treatment time. Doses of SBRT have been reduced to half the level that is necessary (biological equivalent dose, BED of 53 Gy) to achieve tumor ablation in the treatment of other solid tumors (100 Gy BED) to protect the gastrointestinal (GI) tract...
November 2017: Cancer Journal
https://www.readbyqxmd.com/read/29188706/highly-stretchable-and-transparent-electromagnetic-interference-shielding-film-based-on-silver-nanowire-percolation-network-for-wearable-electronics-applications
#19
Jinwook Jung, Habeom Lee, Inho Ha, Hyunmin Cho, Kyun Kyu Kim, Jinhyeong Kwon, Phillip Won, Sukjoon Hong, Seung Hwan Ko
Future electronics are expected to develop into wearable forms and an adequate stretchability is required for the forthcoming wearable electronics considering various motions occurring in human body. Along with stretchability, transparency can increase both the functionality and esthetic features in future wearable electronics. In this paper, we demonstrate, for the first time, a highly stretchable and transparent electromagnetic interference (EMI) shielding layer for wearable electronic applications with silver nanowire percolation network on elastic PDMS substrate...
November 30, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29188241/microscopic-understanding-of-the-conformational-features-of-a-protein-dna-complex
#20
Sandip Mondal, Kaushik Chakraborty, Sanjoy Bandyopadhyay
Protein-DNA interactions play crucial roles in different biological processes. Binding of a protein to its target DNA is the key step at different stages of genetic activities. In this article, we have carried out atomistic molecular dynamics simulations to understand the microscopic conformational and dynamical features of the N-terminal domain of the λ-repressor protein and its operator DNA in their complexed state. The calculations revealed that the overall flexibility of the protein and the DNA components reduces due to complex formation...
November 30, 2017: Physical Chemistry Chemical Physics: PCCP
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