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https://www.readbyqxmd.com/read/27905517/g4ipdb-a-database-for-g-quadruplex-structure-forming-nucleic-acid-interacting-proteins
#1
Subodh Kumar Mishra, Arpita Tawani, Amit Mishra, Amit Kumar
Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ∆Tm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author's name and techniques that were used to detect their interactions...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27904707/prognostic-significance-of-%C3%AE-2-adrenergic-receptor-expression-in-non-small-cell-lung-cancer
#2
Tomohiro Yazawa, Kyoichi Kaira, Kimihiro Shimizu, Akira Shimizu, Keita Mori, Toshiteru Nagashima, Yoichi Ohtaki, Tetsunari Oyama, Akira Mogi, Hiroyuki Kuwano
BACKGROUND: The β2-Adrenergic receptor (β2-AR) is associated with tumor growth and progression. However, the clinical significance of β2-AR expression in patients with non-small cell lung cancer (NSCLC) remains unclear. METHODS: Three hundred twenty-eight patients with surgically resected NSCLC were retrospectively investigated. Tumor sections were stained by immunohistochemistry for assessing β2-AR and Ki-67 expression and microvessel density (MVD), which was using CD34 levels...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27903188/the-role-of-diffusion-tensor-imaging-tractography-for-gamma-knife-thalamotomy-planning
#3
João Gabriel Ribeiro Gomes, Alessandra Augusta Gorgulho, Amanda de Oliveira López, Crystian Wilian Chagas Saraiva, Lucas Petri Damiani, Anderson Martins Pássaro, João Victor Salvajoli, Ludmila de Oliveira Siqueira, Bernardo Peres Salvajoli, Antônio Afonso Ferreira De Salles
OBJECTIVE The role of tractography in Gamma Knife thalamotomy (GK-T) planning is still unclear. Pyramidal tractography might reduce the risk of radiation injury to the pyramidal tract and reduce motor complications. METHODS In this study, the ventralis intermedius nucleus (VIM) targets of 20 patients were bilaterally defined using Iplannet Stereotaxy Software, according to the anterior commissure-posterior commissure (AC-PC) line and considering the localization of the pyramidal tract. The 40 targets and tractography were transferred as objects to the GammaPlan Treatment Planning System (GP-TPS)...
December 2016: Journal of Neurosurgery
https://www.readbyqxmd.com/read/27902594/combined-genotype-and-haplotype-distributions-of-mthfr-c677t-and-a1298c-polymorphisms-a-cross-sectional-descriptive-study-of-13-473-chinese-adult-women
#4
Shujun Fan, Boyi Yang, Xueyuan Zhi, Yanxun Wang, Quanmei Zheng, Guifan Sun
Methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms are, independently and/or in combination, associated with many disorders. However, data on the combined genotype and haplotype distributions of the 2 polymorphisms in Chinese population were limited.We recruited 13,473 adult women from 9 Chinese provinces, collected buccal cell samples, and determined genotypes, to estimate the combined genotype and haplotype distributions of the MTHFR C677T and A1298C polymorphisms.In the total sample, the 6 common combined genotypes were CT/AA (29...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27901539/colloidal-molecules-assembled-from-binary-spheres-under-an-ac-electric-field
#5
Kelley Lynch Heatley, Fuduo Ma, Ning Wu
Colloidal particles are envisioned as analogues of atoms and molecules, however they often lack the complexities present in their counterparts. In this work, we report the assembly of colloidal molecules from a binary mixture of polystyrene spheres (1, 1.6, 2, and 4 μm) under an alternating current electric field. The rich family of assembled oligomers typically consists of a large sphere that is closely surrounded by a number of smaller petal particles, driven by the dipolar attraction between large and small particles...
November 30, 2016: Soft Matter
https://www.readbyqxmd.com/read/27901150/correlation-of-dielectric-electrical-and-magnetic-properties-near-the-magnetic-phase-transition-temperature-of-cobalt-zinc-ferrite
#6
Dhiren K Pradhan, Shalini Kumari, Venkata S Puli, Proloy T Das, Dillip K Pradhan, Ashok Kumar, J F Scott, Ram S Katiyar
Multiferroic composite structures, i.e., composites of magnetostrictive and piezoelectric materials, can be envisioned to achieve the goal of strong room-temperature ME coupling for real practical device applications. Magnetic materials with high magnetostriction, high Néel temperature (TN), high resistivity and large magnetization are required to observe high ME coupling in composite structures. In continuation of our investigations on suitable magnetic candidates for multiferroic composite structures, we have studied the crystal structure, dielectric, transport, and magnetic properties of Co0...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27901138/understanding-the-self-assembly-of-amino-ester-based-benzene-1-3-5-tricarboxamides-using-molecular-dynamics-simulations
#7
Karteek K Bejagam, Richard C Remsing, Michael L Klein, Sundaram Balasubramanian
Amino ester-based benzene-1,3,5-tricarboxamides (BTAs) are widely studied experimentally for their facile self-assembly, which leads to strong three-fold hydrogen bonded supramolecular polymers. Understanding the supramolecular assembly of these BTAs is complicated by the presence of two types of dimers, based on the nature of the intermolecular hydrogen bonding pattern: amide-amide (AA) and amide-carboxylate (AC). AA dimers form three hydrogen bonds between the two molecules, are typical of BTA stacks, and act as a basic building block of assembly...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27900385/aggregation-enhanced-emission-active-tetraphenylbenzene-cored-efficient-blue-light-emitter
#8
Lingzhi Li, Han Nie, Ming Chen, Jingzhi Sun, Anjun Qin, Ben Zhong Tang
A tetraphenylbenzene (TPB) cored luminophore of TPB-AC with aggregation-enhanced emission characteristics was designed and synthesized. TPB-AC could be potentially applied for the fabrication of high performance organic light-emitting diodes (OLEDs) with blue light emission.
November 30, 2016: Faraday Discussions
https://www.readbyqxmd.com/read/27900384/3d-oxalato-bridged-lanthanide-iii-mofs-with-magnetocaloric-magnetic-and-photoluminescence-properties
#9
Muhammad Nadeem Akhtar, Yan-Cong Chen, Murad A AlDamen, Ming-Liang Tong
Four isostructural 3D lanthanide(iii) metal-organic frameworks with the general formula (H6edte)0.5[Ln(III)(ox)2(H2O)] (Ln = Gd (1), Tb (2), Dy (3) and Ho (4); H4edte = N,N,N',N'-tetrakis(2-hydroxyethyl)ethylenediamine) and ox = oxalate have been synthesized from oxalate. These compounds were characterized using single-crystal X-ray diffraction, FTIR and TGA/DTG. The magnetic investigation has been performed for 1-4 and the results reveal that a Gd(iii) containing MOF has the highest magnetic density and exhibits a larger cryogenic magnetocaloric effect (ΔSm = 35...
November 30, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27900310/rockwood-grade-i-and-ii-acromioclavicular-injuries-as-benign-as-commonly-believed
#10
Alexander Scott North
The acromioclavicular (AC) joint is the articulation between the distal clavicle and the acromion process of the scapula. As the upper limb moves, passive motion of the AC joint occurs in three planes, with the AC and coracoclavicular ligaments providing stability. Injuries are common, particularly during contact sports, and are classified using Rockwood's system. Grade I (sprain) and II (rupture) injuries only affect the AC ligaments and are generally managed conservatively. However, recent reports have indicated that long-term outcomes after these injuries are poor, perhaps due to an inadequate period of immobilization preventing complete ligamentous healing...
July 2016: Joints
https://www.readbyqxmd.com/read/27899998/expression-level-of-crkl-and-axl-combined-with-exon-19-deletion-in-egfr-and-alk-status-confer-differential-prognosis-of-lung-adenocarcinoma-subtypes
#11
Yi-Ran Cai, Yu-Jie Dong, Hong-Bo Wu, Da-Ping Yu, Li-Juan Zhou, Dan Su, Li Zhang, Xue-Jing Chen
Non-small cell lung cancer (NSCLC) is a lethal cancer-related disease in population. Adenocarcinoma (AC) is subclassified into several subtypes based on the new classification by the International Association for the Study of Lung Cancer, American Thoracic Society and European Respiratory Society in 2011. Correlation between original expression of Crk-like (CRKL) and anaplastic lymphoma receptor tyrosine kinase in diverse histological components of AC and epidermal growth factor receptor (EGFR) or ALK status was evaluated by immunohistochemistry and sequencing in present study...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899670/the-new-nhgri-ebi-catalog-of-published-genome-wide-association-studies-gwas-catalog
#12
Jacqueline MacArthur, Emily Bowler, Maria Cerezo, Laurent Gil, Peggy Hall, Emma Hastings, Heather Junkins, Aoife McMahon, Annalisa Milano, Joannella Morales, Zoe May Pendlington, Danielle Welter, Tony Burdett, Lucia Hindorff, Paul Flicek, Fiona Cunningham, Helen Parkinson
The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899663/large-scale-analysis-of-microrna-expression-epi-transcriptomic-features-and-biogenesis
#13
Dimitrios M Vitsios, Matthew P Davis, Stijn van Dongen, Anton J Enright
MicroRNAs are important genetic regulators in both animals and plants. They have a range of functions spanning development, differentiation, growth, metabolism and disease. The advent of next-generation sequencing technologies has made it a relatively straightforward task to detect these molecules and their relative expression via sequencing. There are a large number of published studies with deposited datasets. However, there are currently few resources that capitalize on these data to better understand the features, distribution and biogenesis of miRNAs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899658/the-big-data-center-from-deposition-to-integration-to-translation
#14
(no author information available yet)
Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899635/interpro-in-2017-beyond-protein-family-and-domain-annotations
#15
Robert D Finn, Teresa K Attwood, Patricia C Babbitt, Alex Bateman, Peer Bork, Alan J Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A Natale, Marco Necci, Gift Nuka, Christine A Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C Potter, Neil D Rawlings, Nicole Redaschi, Lorna Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger Sutton, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Ioannis Xenarios, Lai-Su Yeh, Siew-Yit Young, Alex L Mitchell
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899630/european-nucleotide-archive-in-2016
#16
Ana Luisa Toribio, Blaise Alako, Clara Amid, Ana Cerdeño-Tarrága, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra Ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rosello, Nicole Silvester, Dmitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899616/the-tissuenet-v-2-database-a-quantitative-view-of-protein-protein-interactions-across-human-tissues
#17
Omer Basha, Ruth Barshir, Moran Sharon, Eugene Lerman, Binyamin F Kirson, Idan Hekselman, Esti Yeger-Lotem
Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. The TissueNet database bridges this gap by associating experimentally-identified PPIs with human tissues that were shown to express both pair-mates. Users can select a protein and a tissue, and obtain a network view of the query protein and its tissue-associated PPIs...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899604/ipd-mhc-2-0-an-improved-inter-species-database-for-the-study-of-the-major-histocompatibility-complex
#18
Giuseppe Maccari, James Robinson, Keith Ballingall, Lisbeth A Guethlein, Unni Grimholt, Jim Kaufman, Chak-Sum Ho, Natasja G de Groot, Paul Flicek, Ronald E Bontrop, John A Hammond, Steven G E Marsh
The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899596/chitars-3-1-the-enhanced-chimeric-transcripts-and-rna-seq-database-matched-with-protein-protein-interactions
#19
Alessandro Gorohovski, Somnath Tagore, Vikrant Palande, Assaf Malka, Dorith Raviv-Shay, Milana Frenkel-Morgenstern
Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922: chimeric transcripts along with 11 714: cancer breakpoints...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899587/temporal-self-regulation-of-transposition-through-host-independent-transposase-rodlet-formation
#20
Lauren E Woodard, Laura M Downes, Yi-Chien Lee, Aparna Kaja, Eyuel S Terefe, Matthew H Wilson
Transposons are highly abundant in eukaryotic genomes, but their mobilization must be finely tuned to maintain host organism fitness and allow for transposon propagation. Forty percent of the human genome is comprised of transposable element sequences, and the most abundant cut-and-paste transposons are from the hAT superfamily. We found that the hAT transposase TcBuster from Tribolium castaneum formed filamentous structures, or rodlets, in human tissue culture cells, after gene transfer to adult mice, and ex vivo in cell-free conditions, indicating that host co-factors or cellular structures were not required for rodlet formation...
November 28, 2016: Nucleic Acids Research
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