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https://www.readbyqxmd.com/read/28088762/the-super-n-motifs-model-a-novel-alignment-free-approach-for-representing-and-comparing-rna-secondary-structures
#1
Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang
MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088356/advancing-the-prediction-accuracy-of-protein-protein-interactions-by-utilizing-evolutionary-information-from-position-specific-scoring-matrix-and-ensemble-classifier
#2
Lei Wang, Zhu-Hong You, Shi-Xiong Xia, Feng Liu, Xing Chen, Xin Yan, Yong Zhou
Protein-Protein Interactions (PPIs) are essential to most biological processes and play a critical role in most cellular functions. With the development of high-throughput biological techniques and in silico methods, a large number of PPI data have been generated for various organisms, but many problems remain unsolved. These factors promoted the development of the in silico methods based on machine learning to predict PPIs. In this study, we propose a novel method by combining ensemble Rotation Forest (RF) classifier and Discrete Cosine Transform (DCT) algorithm to predict the interactions among proteins...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28079128/parallel-meta-3-comprehensive-taxonomical-and-functional-analysis-platform-for-efficient-comparison-of-microbial-communities
#3
Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28076844/sulforaphane-inhibits-cancer-stem-like-cell-properties-and-cisplatin-resistance-through-mir-214-mediated-downregulation-of-c-myc-in-non-small-cell-lung-cancer
#4
Qian-Qian Li, You-Ke Xie, Yue Wu, Lin-Lin Li, Ying Liu, Xiao-Bo Miao, Qiu-Zhen Liu, Kai-Tai Yao, Guang-Hui Xiao
We herein report that sulforaphane (SFN), a potent anti-cancer and well-tolerated dietary compound, inhibits cancer stem-like cell (CSC) properties and enhances therapeutic efficacy of cisplatin in human non-small cell lung cancer (NSCLC). SFN exerted these functions through upregulation of miR-214, which in turn targets the coding region of c-MYC. This finding was further corroborated by our observations that plasmid or lentiviral vector-mediated expression of 3'UTR-less c-MYC cDNA and cisplatin- or doxorubicin-induced endogenous c-MYC accumulation was similarly suppressed by either SFN or miR-214...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28075401/anti-neuroblastoma-properties-of-a-recombinant-sunflower-lectin
#5
Marcela Pinedo, Melanie Genoula, María Ximena Silveyra, André De Oliveira Carvalho, Mariana Regente, Marianela Del Río, Júlia Ribeiro Soares, Valdirene Moreira Gomes, Laura De La Canal
According to their sugar recognition specificity, plant lectins are proposed as bioactive proteins with potential in cancer treatment and diagnosis. Helja is a mannose-specific jacalin-like lectin from sunflower which was shown to inhibit the growth of certain fungi. Here, we report its recombinant expression in a prokaryotic system and its activity in neurobalstoma cells. Helja coding sequence was fused to the pET-32 EK/LIC, the enterokinase/Ligation-independent cloning vector and a 35 kDa protein was obtained in Escherichia coli representing Helja coupled to thioredoxin (Trx)...
January 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28073402/deep-sequencing-analysis-of-tick-borne-encephalitis-virus-from-questing-ticks-at-natural-foci-reveals-similarities-between-quasispecies-pools-of-the-virus
#6
Naveed Asghar, John H-O Pettersson, Patrik Dinnetz, Åshild Andreassen, Magnus Johansson
Every year, tick-borne encephalitis virus (TBEV) causes severe central nervous system infection in 10,000 to 15,000 people in Europe and Asia. TBEV is maintained in the environment by an enzootic cycle that requires a tick vector and a vertebrate host, and the adaptation of TBEV to vertebrate and invertebrate environments is essential for TBEV persistence in nature. This adaptation is facilitated by the error-prone nature of the virus' RNA-dependent RNA polymerase that generates genetically distinct virus variants called quasispecies...
January 10, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28073397/identification-of-new-members-of-the-escherichia-coli-k-12-mg1655-slya-regulon
#7
Thomas Curran, Fatima Abacha, Stephen Hibberd, Matthew Rolfe, Melissa Lacey, Jeffrey Green
SlyA is a member of the MarR family of bacterial transcriptional regulators. Previously, SlyA has been shown to directly regulate only two operons in Escherichia coli K-12 MG1655, fimB and hlyE (clyA). In both cases SlyA activates gene expression by antagonizing repression by the nucleoid associated protein H-NS. Here the transcript profiles of aerobic glucose-limited steady-state chemostat cultures of E. coli K-12 MG1655, slyA mutant and slyA over-expression strains are reported. The transcript profile of the slyA mutant was not significantly different to that of the parent; however, that of the slyA expression strain was significantly different from that of the vector control...
January 10, 2017: Microbiology
https://www.readbyqxmd.com/read/28067165/gene-therapy-in-fanconi-anemia-a-matter-of-time-safety-and-gene-transfer-tool-efficiency
#8
Verhoeyen Els, Francisco José Román Rodríguez, François-Loïc Cosset, Camille Lévy, Paula Rio
Fanconi anemia (FA) is a rare genetic syndrome characterized by progressive marrow failure. Gene therapy by infusion of FA-corrected autologous hematopoietic stem cells (HSCs) may offer a potential cure since it is a monogenetic disease with mutations in the FANC genes, coding for DNA repair enzymes (See review[1]). However, the collection of hCD34 +-cells in FA patients implies particular challenges because of the reduced numbers of progenitor cells present in their bone marrow (BM)[2] or mobilized peripheral blood[3-5]...
January 9, 2017: Current Gene Therapy
https://www.readbyqxmd.com/read/28060725/identification-and-characterization-of-novel-pax8-mutations-in-congenital-hypothyroidism-ch-in-a-chinese-population
#9
Shiguo Liu, Xueqin Wang, Hui Zou, Yinlin Ge, Fang Wang, Yangang Wang, Shengli Yan, Hongfei Xia, Mingzhao Xing
OBJECTIVE: Based on mutations in PAX8 is associated with thyroid dysgenesis. We aim to identify and characterize PAX8 mutations in a large cohort of congenital hypothyroidism(CH) from thyroid dysgenesis in Chinese population. METHODS: We screened 453 unrelated Chinese patients with CH from thyroid dysgenesis for PAX8 mutations by sequencing the whole coding regions of PAX8 on genomic DNA isolated from blood. Cell transfection assays using various vector constructs and induced mutagenesis as well as electrophoretic mobility shift assays were used to investigate the effects of selected mutations on the transcribing and binding activities of PAX8 at the promoters of target genes for thyroglobulin (TG) and thyroperoxidase (TPO)...
January 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28059103/radioiodinated-capsids-facilitate-in-vivo-non-invasive-tracking-of-adeno-associated-gene-transfer-vectors
#10
P Kothari, B P De, B He, A Chen, M J Chiuchiolo, D Kim, A Nikolopoulou, A Amor-Coarasa, J P Dyke, H U Voss, S M Kaminsky, C P Foley, S Vallabhajosula, B Hu, S G DiMagno, D Sondhi, R G Crystal, J W Babich, D Ballon
Viral vector mediated gene therapy has become commonplace in clinical trials for a wide range of inherited disorders. Successful gene transfer depends on a number of factors, of which tissue tropism is among the most important. To date, definitive mapping of the spatial and temporal distribution of viral vectors in vivo has generally required postmortem examination of tissue. Here we present two methods for radiolabeling adeno-associated virus (AAV), one of the most commonly used viral vectors for gene therapy trials, and demonstrate their potential usefulness in the development of surrogate markers for vector delivery during the first week after administration...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28056800/networking-in-microbes-conjugative-elements-and-plasmids-in-the-genus-alteromonas
#11
Mario López-Pérez, Nieves Ramon-Marco, Francisco Rodriguez-Valera
BACKGROUND: To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28056764/temperature-dependent-srna-transcriptome-of-the-lyme-disease-spirochete
#12
Niko Popitsch, Ivana Bilusic, Philipp Rescheneder, Renée Schroeder, Meghan Lybecker
BACKGROUND: Transmission of Borrelia burgdorferi from its tick vector to a vertebrate host requires extensive reprogramming of gene expression. Small regulatory RNAs (sRNA) have emerged in the last decade as important regulators of bacterial gene expression. Despite the widespread observation of sRNA-mediated gene regulation, only one sRNA has been characterized in the Lyme disease spirochete B. burgdorferi. We employed an sRNA-specific deep-sequencing approach to identify the small RNA transcriptome of B...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28055849/hetero-manifold-regularisation-for-cross-modal-hashing
#13
Feng Zheng, Yi Tang, Ling Shao
Recently, cross-modal search has attracted considerable attention but remains a very challenging task because of the integration complexity and heterogeneity of the multi-modal data. To address both challenges, in this paper, we propose a novel method termed hetero-manifold regularisation (HMR) to supervise the learning of hash functions for efficient cross-modal search. A hetero-manifold integrates multiple sub-manifolds defined by homogeneous data with the help of cross-modal supervision information. Taking advantages of the hetero-manifold, the similarity between each pair of heterogeneous data could be naturally measured by three order random walks on this hetero-manifold...
December 28, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28054511/nanoscale-magnetic-ratchets-based-on-shape-anisotropy
#14
Jizhai Cui, Scott Keller, Cheng-Yen Liang, Greg Carman, Christopher Lynch
Controlling magnetization using piezoelectric strain through the magnetoelectric effect offers several orders of magnitude reduction in energy consumption for spintronic applications. However strain is a uniaxial effect and, unlike directional magnetic field or spin-polarized current, cannot induce a full 180° reorientation of the magnetization vector when acting alone. We have engineered novel "peanut" and "cat-eye" shaped nanomagnets on piezoelectric substrates that undergo repeated deterministic 180° magnetization rotations in response to individual electric-field-induced strain pulses by breaking the uniaxial symmetry using shape anisotropy...
January 5, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28049510/identification-of-host-proteins-interacting-with-toxoplasma-gondii-gra15-tggra15-by-yeast-two-hybrid-system
#15
Qing Liu, Fa-Cai Li, Hany M Elsheikha, Miao-Miao Sun, Xing-Quan Zhu
BACKGROUND: Toxoplasma gondii, an obligate intracellular protozoan parasite, possesses the remarkable ability to co-opt host cell machinery in order to maintain its intracellular survival. This parasite can modulate signaling pathways of its host through the secretion of polymorphic effector proteins localized in the rhoptry and dense granule organelles. One of such effectors is T. gondii type II-specific dense granule protein 15, TgGRA15, which activates NF-κB pathway. The aim of the present study was to identify the host interaction partner proteins of TgGRA15...
January 3, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28049109/ci2-for-creating-and-comparing-confidence-intervals-for-time-series-bivariate-plots
#16
David R Mullineaux
Currently no method exists for calculating and comparing the confidence-intervals (CI) for the time-series of a bivariate plot. The study's aim was to develop 'CI2' as a method to calculate the CI on time-series bivariate plots, and to identify if the CI between two bivariate time-series overlap. The test data were the knee and ankle angles from 10 healthy participants running on a motorised standard-treadmill and non-motorised curved-treadmill. For a recommended 10+ trials, CI2 involved calculating 95% confidence-ellipses at each time-point, then taking as the CI the points on the ellipses that were perpendicular to the direction vector between the means of two adjacent time-points...
December 23, 2016: Gait & Posture
https://www.readbyqxmd.com/read/28048238/su-g-tep1-06-fast-gpu-framework-for-four-dimensional-monte-carlo-in-adaptive-intensity-modulated-proton-therapy-impt-for-mobile-tumors
#17
P Botas, C Grassberger, G Sharp, N Qin, X Jia, S Jiang, H Paganetti
PURPOSE: To demonstrate the feasibility of fast Monte Carlo (MC) treatment planning and verification using four-dimensional CT (4DCT) for adaptive IMPT for lung cancer patients. METHODS: A validated GPU MC code, gPMC, has been linked to the patient database at our institution and employed to compute the dose-influence matrices (Dij) on the planning CT (pCT). The pCT is an average of the respiratory motion of the patient. The Dijs and patient structures were fed to the optimizer to calculate a treatment plan...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048189/su-f-j-209-quantification-of-image-guidance-benefit-in-image-guided-radiotherapy-of-cancers
#18
L Zhou, J Deng
PURPOSE: Image-guidance has been widely used in radiation oncology for accurate radiotherapy. The goal of this study is to quantify the benefit of image-guidance in image-guided radiotherapy (IGRT) of cancers. METHODS: In this study, a new index termed image-guidance benefit (IGB), was proposed to quantify the benefit of image-guidance in cancer radiotherapy. It is calculated as a ratio of the square sum of dose differences between planning dose matrix and actual delivery dose matrix post image-guidance to the square sum of dose summation between the two matrixes, summing over all dose scoring voxels...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048172/mo-fg-bra-01-4d-monte-carlo-simulations-for-verification-of-dose-delivered-to-a-moving-anatomy
#19
S Gholampourkashi, J E Cygler, J Belec, M Vujicic, Heath
PURPOSE: To validate 4D Monte Carlo (MC) simulations of dose delivery by an Elekta Agility linear accelerator to a moving phantom. METHODS: Monte Carlo simulations were performed using the 4DdefDOSXYZnrc/EGSnrc user code which samples a new geometry for each incident particle and calculates the dose in a continuously moving anatomy. A Quasar respiratory motion phantom with a lung insert containing a 3 cm diameter tumor was used for dose measurements on an Elekta Agility linac with the phantom in stationary and moving states...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047382/mo-fg-campus-tep1-02-facial-recognition-and-recall-using-kinect-v2-for-patient-verification
#20
E Silverstein, M Snyder
PURPOSE: Investigate capability and accuracy of the Kinect v2 camera for facial recognition to use as a tool for patient check-in upon arrival, as well as patient verification when entering treatment vault. METHODS: The Kinect software has a native facial recognition feature which recognizes major facial landmarks (eyes, nose, mouth, etc). 1347 facial vertices are automatically generated, each located at a specific facial point at standardized distances between points...
June 2016: Medical Physics
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