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https://www.readbyqxmd.com/read/27905547/in-silico-mapping-of-protein-unfolding-mutations-for-inherited-disease
#1
Caitlyn L McCafferty, Yuri V Sergeev
The effect of disease-causing missense mutations on protein folding is difficult to evaluate. To understand this relationship, we developed the unfolding mutation screen (UMS) for in silico evaluation of the severity of genetic perturbations at the atomic level of protein structure. The program takes into account the protein-unfolding curve and generates propensities using calculated free energy changes for every possible missense mutation at once. These results are presented in a series of unfolding heat maps and a colored protein 3D structure to show the residues critical to the protein folding and are available for quick reference...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900458/utility-of-whole-lesion-adc-histogram-metrics-for-assessing-the-malignant-potential-of-pancreatic-intraductal-papillary-mucinous-neoplasms-ipmns
#2
David H Hoffman, Justin M Ream, Christina H Hajdu, Andrew B Rosenkrantz
PURPOSE: To evaluate whole-lesion ADC histogram metrics for assessing the malignant potential of pancreatic intraductal papillary mucinous neoplasms (IPMNs), including in comparison with conventional MRI features. METHODS: Eighteen branch-duct IPMNs underwent MRI with DWI prior to resection (n = 16) or FNA (n = 2). A blinded radiologist placed 3D volumes-of-interest on the entire IPMN on the ADC map, from which whole-lesion histogram metrics were generated. The reader also assessed IPMN size, mural nodularity, and adjacent main-duct dilation...
November 30, 2016: Abdominal Radiology
https://www.readbyqxmd.com/read/27899675/jet2-viewer-a-database-of-predicted-multiple-possibly-overlapping-protein-protein-interaction-sites-for-pdb-structures
#3
Hughes Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone
The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET(2) at large-scale on more than 20 000 chains. JET(2) strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET(2) analyses...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899590/different%C3%A2-enhancer-classes-in-drosophila-bind-distinct-architectural-proteins-and-mediate-unique-chromatin-interactions-and-3d-architecture
#4
Caelin Cubeñas-Potts, M Jordan Rowley, Xiaowen Lyu, Ge Li, Elissa P Lei, Victor G Corces
Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and developmental enhancers (dCP). We hypothesized that the two enhancer classes are occupied by distinct architectural proteins, affecting their enhancer-promoter contacts. By evaluating ChIP-seq occupancy of architectural proteins, typical enhancer-associated proteins, and histone modifications, we determine that both enhancer classes are enriched for RNA Polymerase II, CBP, and architectural proteins but there are also distinctions...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895710/in-situ-label-free-imaging-of-hemicellulose-in-plant-cell-walls-using-stimulated-raman-scattering-microscopy
#5
Yining Zeng, John M Yarbrough, Ashutosh Mittal, Melvin P Tucker, Todd B Vinzant, Stephen R Decker, Michael E Himmel
BACKGROUND: Plant hemicellulose (largely xylan) is an excellent feedstock for renewable energy production and second only to cellulose in abundance. Beyond a source of fermentable sugars, xylan constitutes a critical polymer in the plant cell wall, where its precise role in wall assembly, maturation, and deconstruction remains primarily hypothetical. Effective detection of xylan, particularly by in situ imaging of xylan in the presence of other biopolymers, would provide critical information for tackling the challenges of understanding the assembly and enhancing the liberation of xylan from plant materials...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27892880/mri-cross-sectional-atlas-of-normal-canine-cervical-musculoskeletal-structure
#6
M Alizadeh, C Zindl, M J Allen, G G Knapik, N Fitzpatrick, W S Marras
Although magnetic resonance imaging (MRI) has been increasingly used as a diagnostic tool for cervical spine injuries in canines, a comprehensive normal MRI anatomy of the canine cervical spine muscles is lacking. Therefore, the purpose of this study was to build a magnetic resonance imaging atlas of the normal cross sectional anatomy of the muscles of the canine cervical spine. MRI scans were performed on a canine cadaver using a combination of T1 and T2-weighted images in the transverse, sagittal and dorsal planes acquired at a slice thickness of 1mm...
September 30, 2016: Research in Veterinary Science
https://www.readbyqxmd.com/read/27891668/systematic-mapping-of-the-subchondral-bone-3d-microarchitecture-in-the-human-tibial-plateau-variations-with-joint-alignment
#7
Bryant C Roberts, Dominic Thewlis, Lucian B Solomon, Graham Mercer, Karen J Reynolds, Egon Perilli
Tibial subchondral bone plays an important role in knee osteoarthritis (OA). Microarchitectural characterization of subchondral bone plate (SBP), underlying subchondral trabecular bone (STB) and relationships between these compartments, however, is limited. The aim of this study was to characterize the spatial distribution of SBP thickness, SBP porosity and STB microarchitecture, and relationships among them, in OA tibiae of varying joint alignment. Twenty-five tibial plateaus from end-stage knee-OA patients, with varus (n = 17) or non-varus (n = 8) alignment were micro-CT scanned (17 μm/voxel)...
November 7, 2016: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/27888153/three-dimensional-black-blood-t2-mapping-with-compressed-sensing-and-data-driven-parallel-imaging-in-the-carotid-artery
#8
Jianmin Yuan, Ammara Usman, Scott A Reid, Kevin F King, Andrew J Patterson, Jonathan H Gillard, Martin J Graves
PURPOSE: To develop a 3D black-blood T2 mapping sequence with a combination of compressed sensing (CS) and parallel imaging (PI) for carotid wall imaging. MATERIALS AND METHODS: A 3D black-blood fast-spin-echo (FSE) sequence for T2 mapping with CS and PI was developed and validated. Phantom experiments were performed to assess T2 accuracy using a Eurospin Test Object, with different combination of CS and PI acceleration factors. A 2D multi-echo FSE sequence was used as a reference to evaluate the accuracy...
November 22, 2016: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/27886002/three-dimensional-vs-two-dimensional-shear-wave-elastography-of-the-testes-preliminary-study-on-a-healthy-collective
#9
J Marcon, M Trottmann, J Rübenthaler, M D'Anastasi, C G Stief, M F Reiser, D A Clevert
INTRODUCTION: Shear wave elastography (SWE) and its derivative Supersonic Shear Imaging (SSI) are newer techniques for the determination of tissue elasticity by measuring the velocity of generated shear waves (SWV), which correlates positively with tissue stiffness.The techniques are integrated into many modern ultrasound systems and have been examined in the evaluation of viscoelastic properties of different organ systems. Two-dimensional shear wave elastography (2D SWE) of the testes has been found to be a useful tool in recent studies which included the determination of standard values in healthy volunteers...
November 23, 2016: Clinical Hemorheology and Microcirculation
https://www.readbyqxmd.com/read/27885742/catheter-ablation-in-the-right-ventricular-outflow-tract-associated-with-occlusion-of-left-anterior-descending-coronary-artery
#10
Daniel Benhayon, Eyal Nof, William W Chik, Francis Marchlinski
Major vessel injury during right ventricular outflow tract ablation is not something widely recognized, and routine evaluation of the left anterior descending artery (LAD) location in relation to the septal right ventricle is not routinely performed. In the present article we report a case of acute LAD occlusion after RVOT ablation and then illustrate the intimately close relationship of the left anterior descending artery to the anterior septal site of the RVOT (∼ 2-3 cm under the pulmonic valve), using a combination of intracardiac echocardiography and 3D electroanatomical mapping (EAM) recorded during a second case, in order to specifically point to the area at risk...
November 25, 2016: Journal of Cardiovascular Electrophysiology
https://www.readbyqxmd.com/read/27885540/automatic-abdominal-multi-organ-segmentation-using-deep-convolutional-neural-network-and-time-implicit-level-sets
#11
Peijun Hu, Fa Wu, Jialin Peng, Yuanyuan Bao, Feng Chen, Dexing Kong
PURPOSE: Multi-organ segmentation from CT images is an essential step for computer-aided diagnosis and surgery planning. However, manual delineation of the organs by radiologists is tedious, time-consuming and poorly reproducible. Therefore, we propose a fully automatic method for the segmentation of multiple organs from three-dimensional abdominal CT images. METHODS: The proposed method employs deep fully convolutional neural networks (CNNs) for organ detection and segmentation, which is further refined by a time-implicit multi-phase evolution method...
November 24, 2016: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/27884788/the-virtual-dissecting-room-creating-highly-detailed-anatomy-models-for-educational-purposes
#12
Marijn Zilverschoon, Koen L Vincken, Ronald L A W Bleys
INTRODUCTION: Virtual 3D models are powerful tools for teaching anatomy. At the present day, there are a lot of different digital anatomy models, most of these commercial applications are based on a 3D model of a human body reconstructed from images with a 1 millimeter intervals. The use of even smaller intervals may result in more details and more realistic appearances of 3D anatomy models. The aim of this study was to create a realistic and highly detailed 3D model of the hand and wrist based on small interval cross-sectional images, suitable for undergraduate and postgraduate teaching purposes with the possibility to perform a virtual dissection in an educational application...
November 21, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27884018/blood-transfusion-during-radical-chemo-radiotherapy-does-not-reduce-tumour-hypoxia-in-squamous-cell-cancer-of-the-head-and-neck
#13
Liam Welsh, Rafal Panek, Angela Riddell, Kee Wong, Martin O Leach, Mahvash Tavassoli, Durdana Rahman, Maria Schmidt, Tara Hurley, Lorna Grove, Thomas Richards, Dow-Mu Koh, Christopher Nutting, Kevin Harrington, Kate Newbold, Shreerang Bhide
BACKGROUND: Patients with head and neck squamous cell carcinoma (HNSCC) undergoing radical chemo-radiation (CRT) frequently receive transfusion with packed red cells (PRCT) during radiotherapy on the basis that PRCT increases tumour oxygenation and overcomes hypoxia-induced radio-resistance. This is likely to be a significant oversimplification given the fact that tumour hypoxia is the result of several intrinsic and extrinsic factors, including many that are not directly related to serum haemoglobin (Hb)...
November 24, 2016: British Journal of Cancer
https://www.readbyqxmd.com/read/27883982/exocranial-surfaces-for-sex-assessment-of-the-human-cranium
#14
Barbora Musilová, Ján Dupej, Jana Velemínská, Kathia Chaumoitre, Jaroslav Bruzek
Determination of sex is one of the most important and challenging disciplines in biological anthropology. Creating a robust tool for sexing crania is crucial for forensic anthropology, especially in this period of migration, travel, and globalization, when different populations are mixed together in one region. Many different approaches to sex estimation using the skull have been published; however, population specificity and oscillation of variable sexual dimorphism typically reduces their effectiveness. The aim of this study was to create a robust classifier using virtual anthropology without the use of a CT scanner...
November 11, 2016: Forensic Science International
https://www.readbyqxmd.com/read/27883250/3d-tract-specific-local-and-global-analysis-of-white-matter-integrity-in-alzheimer-s-disease
#15
Yan Jin, Chao Huang, Madelaine Daianu, Liang Zhan, Emily L Dennis, Robert I Reid, Clifford R Jack, Hongtu Zhu, Paul M Thompson
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterized by progressive decline in memory and other aspects of cognitive function. Diffusion-weighted imaging (DWI) offers a non-invasive approach to delineate the effects of AD on white matter (WM) integrity. Previous studies calculated either some summary statistics over regions of interest (ROI analysis) or some statistics along mean skeleton lines (Tract Based Spatial Statistic [TBSS]), so they cannot quantify subtle local WM alterations along major tracts...
November 24, 2016: Human Brain Mapping
https://www.readbyqxmd.com/read/27881953/connectomic-analysis-of-brain-networks-novel-techniques-and-future-directions
#16
REVIEW
J Leonie Cazemier, Francisco Clascá, Paul H E Tiesinga
Brain networks, localized or brain-wide, exist only at the cellular level, i.e., between specific pre- and post-synaptic neurons, which are connected through functionally diverse synapses located at specific points of their cell membranes. "Connectomics" is the emerging subfield of neuroanatomy explicitly aimed at elucidating the wiring of brain networks with cellular resolution and a quantified accuracy. Such data are indispensable for realistic modeling of brain circuitry and function. A connectomic analysis, therefore, needs to identify and measure the soma, dendrites, axonal path, and branching patterns together with the synapses and gap junctions of the neurons involved in any given brain circuit or network...
2016: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/27880735/automatic-3d-liver-segmentation-based-on-deep-learning-and-globally-optimized-surface-evolution
#17
Peijun Hu, Fa Wu, Jialin Peng, Ping Liang, Dexing Kong
The detection and delineation of the liver from abdominal 3D computed tomography (CT) images are fundamental tasks in computer-assisted liver surgery planning. However, automatic and accurate segmentation, especially liver detection, remains challenging due to complex backgrounds, ambiguous boundaries, heterogeneous appearances and highly varied shapes of the liver. To address these difficulties, we propose an automatic segmentation framework based on 3D convolutional neural network (CNN) and globally optimized surface evolution...
November 23, 2016: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27879651/prediction-of-protein-protein-interactions-by-evidence-combining-methods
#18
REVIEW
Ji-Wei Chang, Yan-Qing Zhou, Muhammad Tahir Ul Qamar, Ling-Ling Chen, Yu-Duan Ding
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of cell functions. Several experimental techniques operating in vivo or in vitro have made significant contributions to screening a large number of protein interaction partners, especially high-throughput experimental methods. However, computational approaches for PPI predication supported by rapid accumulation of data generated from experimental techniques, 3D structure definitions, and genome sequencing have boosted the map sketching of PPIs...
November 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27877188/identification-of-genomic-associations-for-adult-plant-resistance-in-the-background-of-popular-south-asian-wheat-cultivar-pbw343
#19
Huihui Li, Sukhwinder Singh, Sridhar Bhavani, Ravi P Singh, Deepmala Sehgal, Bhoja R Basnet, Prashant Vikram, Juan Burgueno-Ferreira, Julio Huerta-Espino
Rusts, a fungal disease as old as its host plant wheat, has caused havoc for over 8000 years. As the rust pathogens can evolve into new virulent races which quickly defeat the resistance that primarily rely on race specificity, adult plant resistance (APR) has often been found to be race non-specific and hence is considered to be a more reliable and durable strategy to combat this malady. Over decades sets of donor lines have been identified at International Maize and Wheat Improvement Center (CIMMYT) representing a wide range of APR sources in wheat...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27875202/hybrid-tactile-tangible-interaction-for-3d-data-exploration
#20
Lonni Besancon, Paul Issartel, Mehdi Ammi, Tobias Isenberg
We present the design and evaluation of an interface that combines tactile and tangible paradigms for 3D visualization. While studies have demonstrated that both tactile and tangible input can be efficient for a subset of 3D manipulation tasks, we reflect here on the possibility to combine the two complementary input types. Based on a field study and follow-up interviews, we present a conceptual framework of the use of these different interaction modalities for visualization both separately and combined-focusing on free exploration as well as precise control...
January 2017: IEEE Transactions on Visualization and Computer Graphics
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