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https://www.readbyqxmd.com/read/28720707/intrinsically-disordered-chromatin-protein-nupr1-binds-to-the-c-terminal-region-of-polycomb-ring1b
#1
Patricia Santofimia-Castaño, Bruno Rizzuti, Ángel L Pey, Philippe Soubeyran, Miguel Vidal, Raúl Urrutia, Juan L Iovanna, José L Neira
Intrinsically disordered proteins (IDPs) are ubiquitous in eukaryotes, and they are often associated with diseases in humans. The protein NUPR1 is a multifunctional IDP involved in chromatin remodeling and in the development and progression of pancreatic cancer; however, the details of such functions are unknown. Polycomb proteins are involved in specific transcriptional cascades and gene silencing. One of the proteins of the Polycomb complex is the Ring finger protein 1 (RING1). RING1 is related to aggressive tumor features in multiple cancer types...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28719247/telehealth-in-schools-using-a-systematic-educational-model-based-on-fiction-screenplays-interactive-documentaries-and-three-dimensional-computer-graphics
#2
Diogo Julien Miranda, Chao Lung Wen
BACKGROUND: Preliminary studies suggest the need of a global vision in academic reform, leading to education re-invention. This would include problem-based education using transversal topics, developing of thinking skills, social interaction, and information-processing skills. We aimed to develop a new educational model in health with modular components to be broadcast and applied as a tele-education course. MATERIALS AND METHODS: We developed a systematic model based on a "Skills and Goals Matrix" to adapt scientific contents on fictional screenplays, three-dimensional (3D) computer graphics of the human body, and interactive documentaries...
July 18, 2017: Telemedicine Journal and E-health: the Official Journal of the American Telemedicine Association
https://www.readbyqxmd.com/read/28719194/molecular-modeling-of-the-major-dna-adduct-formed-from-the-food-mutagen-ochratoxin-a-in-nari-2-base-deletion-duplexes-impact-of-sequence-context-and-adduct-ionization-on-conformational-preference-and-mutagenicity
#3
Preetleen Kathuria, Purshotam Sharma, Richard A Manderville, Stacey D Wetmore
Exposure to ochratoxin A (OTA), a possible human carcinogen, leads to many different DNA mutations. As a first step toward understanding the structural basis of OTA-induced mutagenicity, the present work uses a robust computational approach and a slipped mutagenic intermediate model previously studied for C(8)-dG aromatic amine adducts to analyze the conformational features of post-replication 2-base deletion DNA duplexes containing OT-dG, the major OTA lesion at the C(8) position of guanine. Specifically, a total of 960 ns of molecular dynamics simulations (excluding trial simulations) were carried out on four OT-dG ionization states in three sequence contexts within oligomers containing the NarI recognition sequence, a known hotspot for deletion mutations induced by related adducts formed from known carcinogens...
July 18, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28719062/immersive-virtual-reality-as-a-teaching-tool-for-neuroanatomy
#4
Katelyn Stepan, Joshua Zeiger, Stephanie Hanchuk, Anthony Del Signore, Raj Shrivastava, Satish Govindaraj, Alfred Iloreta
BACKGROUND: Three-dimensional (3D) computer modeling and interactive virtual reality (VR) simulation are validated teaching techniques used throughout medical disciplines. Little objective data exists supporting its use in teaching clinical anatomy. Learner motivation is thought to limit the rate of utilization of such novel technologies. The purpose of this study is to evaluate the effectiveness, satisfaction, and motivation associated with immersive VR simulation in teaching medical students neuroanatomy...
July 18, 2017: International Forum of Allergy & Rhinology
https://www.readbyqxmd.com/read/28717801/mimicking-arterial-thrombosis-in-a-3d-printed-microfluidic-in-vitro-vascular-model-based-on-computed-tomography-angiography-data
#5
Pedro F Costa, Hugo J Albers, John E A Linssen, Heleen H T Middelkamp, Linda van der Hout, Robert Passier, Albert van den Berg, Jos Malda, Andries D van der Meer
Arterial thrombosis is the main instigating factor of heart attacks and strokes, which result in over 14 million deaths worldwide every year. The mechanism of thrombosis involves factors from the blood and the vessel wall, and it also relies strongly on 3D vessel geometry and local blood flow patterns. Microfluidic chip-based vascular models allow controlled in vitro studies of the interaction between vessel wall and blood in thrombosis, but until now, they could not fully recapitulate the 3D geometry and blood flow patterns of real-life healthy or diseased arteries...
July 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28716627/membrane-proteins-structures-a-review-on-computational-modeling-tools
#6
REVIEW
Jose G Almeida, Antonio J Preto, Panagiotis I Koukos, Alexandre M J J Bonvin, Irina S Moreira
BACKGROUND: Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28714502/insights-into-the-rna-binding-mechanism-of-human-l1-orf1p-a-molecular-dynamics-study
#7
Muthukumaran Rajagopalan, Sangeetha Balasubramanian, Amutha Ramaswamy
The recognition and binding of nucleic acids by ORF1p, an L1 retrotransposon protein, have not yet been clearly understood due to the lack of structural knowledge. The present study attempts to identify the probable single-stranded RNA binding pathway of trimeric ORF1p using computational methods like ligand mapping methodology combined with molecular dynamics simulations. Using the ligand mapping methodology, the possible RNA interacting sites on the surface of the trimeric ORF1p were identified. The crystal structure of the ORF1p timer and an RNA molecule of 29 nucleotide bases in length were used to generate the structure of the ORF1p complex based on information on predicted binding sites as well as the functional states of the CTD...
July 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28713784/identification-of-novel-and-efficacious-chemical-compounds-that-disturb-influenza-a-virus-entry-in-vitro
#8
Hany Khalil, Tamer El Malah, Ahmed I Abd El Maksoud, Ibrahim El Halfawy, Ahmed A El Rashedy, Mahmoud El Hefnawy
Influenza A virus is a negative RNA stranded virus of the family Orthomyxoviridae, and represents a major public health threat, compounding existing disease conditions. Influenza A virus replicates rapidly within its host and the segmented nature of its genome facilitates re-assortment, whereby whole genes are exchanged between influenza virus subtypes during replication. Antiviral medications are important pharmacological tools in influenza virus prophylaxis and therapy. However, the use of currently available antiviral is impeded by sometimes high levels of resistance in circulating virus strains...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28711988/emotion-recognition-based-on-eeg-features-in-movie-clips-with-channel-selection
#9
Mehmet Siraç Özerdem, Hasan Polat
Emotion plays an important role in human interaction. People can explain their emotions in terms of word, voice intonation, facial expression, and body language. However, brain-computer interface (BCI) systems have not reached the desired level to interpret emotions. Automatic emotion recognition based on BCI systems has been a topic of great research in the last few decades. Electroencephalogram (EEG) signals are one of the most crucial resources for these systems. The main advantage of using EEG signals is that it reflects real emotion and can easily be processed by computer systems...
July 15, 2017: Brain Informatics
https://www.readbyqxmd.com/read/28711760/investigation-of-the-binding-free-energies-of-fda-approved-drugs-against-subtype-b-and-c-sa-hiv-pr-oniom-approach
#10
Z K Sanusi, T Govender, G E M Maguire, S B Maseko, J Lin, H G Kruger, B Honarparvar
Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B...
June 29, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28710037/rna-editing-independently-occurs-at-three-mir-376a-1-sites-and-may-compromise-the-stability-of-the-microrna-hairpin
#11
Alicia Gallego, Diego A Hartasánchez, Marina Brasó-Vives, Eva Garcia-Ramallo, Maria Lopez-Valenzuela, Neus Baena, Miriam Guitart, Hugo Fernández-Bellon, Ivanela Kondova, Ronald Bontrop, Yukio Kawahara, Yolanda Espinosa-Parrilla
RNA editing is being recognized as an important post-transcriptional mechanism that may have crucial roles in introducing genetic variation and phenotypic diversity. Despite microRNA editing recurrence, defining its biological relevance is still under extended debate. To better understand microRNA editing function and regulation we performed an exhaustive characterization of the A-to-I site-specific patterns in mir-376a-1, a mammalian microRNA which RNA editing is involved in the regulation of development and in disease...
July 11, 2017: Gene
https://www.readbyqxmd.com/read/28710008/identifying-synthetic-lethal-targets-using-crispr-cas9-system
#12
Jaspreet Kaur Dhanjal, Navaneethan Radhakrishnan, Durai Sundar
Synthetic lethality occurs when co-occurrence of two genetic events is unfavorable for the survival of the cell or organism. The conventional approach of high throughput screening of synthetic lethal targets using chemical compounds has been replaced by RNAi technology. CRISPR/Cas9, an RNA guided endonuclease system is the most recent technology for this work. Here, we have discussed the major considerations involved in designing a CRISPR/Cas9 based screening experiment for identification of synthetic lethal targets...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28706303/memristive-neural-network-for-on-line-learning-and-tracking-with-brain-inspired-spike-timing-dependent-plasticity
#13
G Pedretti, V Milo, S Ambrogio, R Carboni, S Bianchi, A Calderoni, N Ramaswamy, A S Spinelli, D Ielmini
Brain-inspired computation can revolutionize information technology by introducing machines capable of recognizing patterns (images, speech, video) and interacting with the external world in a cognitive, humanlike way. Achieving this goal requires first to gain a detailed understanding of the brain operation, and second to identify a scalable microelectronic technology capable of reproducing some of the inherent functions of the human brain, such as the high synaptic connectivity (~10(4)) and the peculiar time-dependent synaptic plasticity...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28704900/examination-of-an-audiologist-s-response-to-patient-s-expression-of-symptoms-a-pilot-study
#14
Ashley L Dockens, Monica L Bellon-Harn, Erin S Burns, Vinaya Manchaiah, Orlando Hinojosa
This pilot study explores audiologist-patient interactions during initial evaluations or consultations. In particular, an audiologist's response to patient symptoms is examined. Conversations between audiologist and patients were recorded using a digital recorder, which were transcribed, and analyzed using the Codes for Human Analysis of Transcripts and Child Language Analysis computer programs. Mean length of turn and frequency of utterances related to explicit discussion or description of symptoms or the patient's interpretation of symptoms was determined...
July 2017: Journal of Audiology & Otology
https://www.readbyqxmd.com/read/28702735/is-the-extrastriate-body-area-part-of-the-dorsal-visuomotor-stream
#15
Marius Zimmermann, Rogier B Mars, Floris P de Lange, Ivan Toni, Lennart Verhagen
The extrastriate body area (EBA) processes visual information about body parts, and it is considered one among a series of category-specific perceptual modules distributed across the occipito-temporal cortex. However, recent evidence raises the possibility that EBA might also provide an interface between perception and action, linking the ventral and dorsal streams of visual information processing. Here, we assess anatomical evidence supporting this possibility. We localise EBA in individual subjects using a perceptual task and compare the characteristics of its functional and structural connectivity to those of two perceptual areas, the lateral occipital complex (LOC) and the fusiform body area (FBA), separately for each hemisphere...
July 12, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/28701198/scaffolding-of-long-read-assemblies-using-long-range-contact-information
#16
Jay Ghurye, Mihai Pop, Sergey Koren, Derek Bickhart, Chen-Shan Chin
BACKGROUND: Long read technologies have revolutionized de novo genome assembly by generating contigs orders of magnitude longer than that of short read assemblies. Although assembly contiguity has increased, it usually does not reconstruct a full chromosome or an arm of the chromosome, resulting in an unfinished chromosome level assembly. To increase the contiguity of the assembly to the chromosome level, different strategies are used which exploit long range contact information between chromosomes in the genome...
July 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28699533/class-a-gpcrs-structure-function-modeling-and-structure-based-ligand-design
#17
Xiaojing Cong, Jérémie Topin, Jérôme Golebiowski
G protein-coupled receptors (GPCRs), especially the class A, are the most heavily investigated drug targets in the pharmaceutical industry. Tremendous efforts have been made by both industry and academia to understand the molecular structure and function of this large family of transmembrane proteins. Our understanding in GPCR activation has evolved from the classical inactive-active two-state model to a complex view of GPCR conformational ensemble associated with multiple interacting partners such as ligands, allosteric modulators, ions and downstream signaling proteins...
July 10, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28699527/bioinformatics-approaches-to-profile-the-tumor-microenvironment-for-immunotherapeutic-discovery
#18
Trevor Clancy, Ruth Dannenfelser, Olga Troyanskaya, Karl Johan Malmberg, Eivind Hovig, Vessela Kristensen
In the microenvironment of a malignancy, tumor cells do not exist in isolation, but rather in a diverse ecosystem consisting not only of heterogeneous tumor-cell clones, but also normal cell types such as fibroblasts, vasculature, and an extensive pool of immune cells at numerous possible stages of activation and differentiation. This results in a complex interplay of diverse cellular signaling systems, where the immune cell component is now established to influence cancer progression and therapeutic response...
July 10, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28699046/optical-clearing-and-fluorescence-deep-tissue-imaging-for-3d-quantitative-analysis-of-the-brain-tumor-microenvironment
#19
Tonny Lagerweij, Sophie A Dusoswa, Adrian Negrean, Esther M L Hendrikx, Helga E de Vries, Jeroen Kole, Juan J Garcia-Vallejo, Huibert D Mansvelder, W Peter Vandertop, David P Noske, Bakhos A Tannous, René J P Musters, Yvette van Kooyk, Pieter Wesseling, Xi Wen Zhao, Thomas Wurdinger
BACKGROUND: Three-dimensional visualization of the brain vasculature and its interactions with surrounding cells may shed light on diseases where aberrant microvascular organization is involved, including glioblastoma (GBM). Intravital confocal imaging allows 3D visualization of microvascular structures and migration of cells in the brain of mice, however, with limited imaging depth. To enable comprehensive analysis of GBM and the brain microenvironment, in-depth 3D imaging methods are needed...
July 11, 2017: Angiogenesis
https://www.readbyqxmd.com/read/28692061/a-causal-account-of-the-brain-network-computations-underlying-strategic-social-behavior
#20
Christopher A Hill, Shinsuke Suzuki, Rafael Polania, Marius Moisa, John P O'Doherty, Christian C Ruff
During competitive interactions, humans have to estimate the impact of their own actions on their opponent's strategy. Here we provide evidence that neural computations in the right temporoparietal junction (rTPJ) and interconnected structures are causally involved in this process. By combining inhibitory continuous theta-burst transcranial magnetic stimulation with model-based functional MRI, we show that disrupting neural excitability in the rTPJ reduces behavioral and neural indices of mentalizing-related computations, as well as functional connectivity of the rTPJ with ventral and dorsal parts of the medial prefrontal cortex...
July 10, 2017: Nature Neuroscience
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