keyword
MENU ▼
Read by QxMD icon Read
search

vector coding

keyword
https://www.readbyqxmd.com/read/29791590/lncrna-ccat1-promotes-cell-proliferation-migration-and-invasion-by-down-regulation-of-mir-143-in-ftc-133-thyroid-carcinoma-cell-line
#1
Tianzheng Yang, Hongyan Zhai, Ruihong Yan, Zhenhu Zhou, Lei Gao, Luqing Wang
Thyroid cancer is a common malignant tumor. Long non-coding RNA colon cancer-associated transcript 1 (lncRNA CCAT1) is highly expressed in many cancers; however, the molecular mechanism of CCAT1 in thyroid cancer remains unclear. Hence, this study aimed to investigate the effect of CCAT1 on human thyroid cancer cell line FTC-133. FTC-133 cells were transfected with CCAT1 expressing vector, CCAT1 shRNA, miR-143 mimic, and miR-143 inhibitor, respectively. After different treatments, cell viability, proliferation, migration, invasion, and apoptosis were measured...
2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/29787571/rnai-screening-of-subtracted-transcriptomes-reveals-tumor-suppression-by-taurine-activated-gabaa-receptors-involved-in-volume-regulation
#2
Camiel L C Wielders, Pim van Nierop, Tinke L Vormer, Floris Foijer, Joanne Verheij, Johannes C Lodder, Jesper B Andersen, Huibert D Mansvelder, Hein Te Riele
To identify coding and non-coding suppressor genes of anchorage-independent proliferation by efficient loss-of-function screening, we have developed a method for enzymatic production of low complexity shRNA libraries from subtracted transcriptomes. We produced and screened two LEGO (Low-complexity by Enrichment for Genes shut Off) shRNA libraries that were enriched for shRNA vectors targeting coding and non-coding polyadenylated transcripts that were reduced in transformed Mouse Embryonic Fibroblasts (MEFs)...
2018: PloS One
https://www.readbyqxmd.com/read/29780749/-rhipicephalus-bursa-sialotranscriptomic-response-to-blood-feeding-and-babesia-ovis-infection-identification-of-candidate-protective-antigens
#3
Sandra Antunes, Joana Couto, Joana Ferrolho, Fábio Rodrigues, João Nobre, Ana S Santos, M Margarida Santos-Silva, José de la Fuente, Ana Domingos
Ticks are among the most prevalent blood-feeding arthropods, and they act as vectors and reservoirs for numerous pathogens. Sialotranscriptomic characterizations of tick responses to blood feeding and pathogen infections can offer new insights into the molecular interplay occurring at the tick-host-pathogen interface. In the present study, we aimed to identify and characterize Rhipicephalus bursa salivary gland (SG) genes that were differentially expressed in response to blood feeding and Babesia ovis infection...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29771412/lncrna-cche1-in-the-proliferation-and-apoptosis-of-gastric-cancer-cells
#4
G Xu, Y Zhang, N Li, J-B Zhang, R Xu
OBJECTIVE: We aimed at investigating the effects of long non-coding RNA (lncRNA) CCHE1 on proliferation and apoptosis of gastric cancer cells. MATERIALS AND METHODS: qRT-PCR method was used to detect lncRNA CCHE1 in cancer cell lines. Cells with relative expression were selected to change the expression by transfecting with corresponding lentiviral vector, and nonsense transfection group and blank control group were also constructed; cell counting kit-8 (CCK-8) method was used to assess cell proliferation activity; colony formation assay was used to evaluate the rate of cell cloning; flow cytometry assay was used to determine the apoptosis rate and cell cycle...
May 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29771290/single-cell-clustering-based-on-cell-pair-differentiability-correlation-and-variance-analysis
#5
Hao Jiang, Lydia Sohn, Haiyan Huang, Luonan Chen
Motivation: The rapid advancement of single cell technologies has shed new light on the complex mechanisms of cellular heterogeneity. Identification of intercellular transcriptomic heterogeneity is one of the most critical tasks in single-cell RNA-sequencing studies. Results: We propose a new cell similarity measure based on cell-pair differentiability correlation, which is derived from gene differential pattern among all cell pairs. Through plugging into the framework of hierarchical clustering with this new measure, we further develop a variance analysis based clustering algorithm 'Corr' that can determine cluster number automatically and identify cell types accurately...
May 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29767230/competing-endogenous-rna-regulatory-network-in-papillary-thyroid-carcinoma
#6
Shouhua Chen, Xiaobin Fan, He Gu, Lili Zhang, Wenhua Zhao
The present study aimed to screen all types of RNAs involved in the development of papillary thyroid carcinoma (PTC). RNA‑sequencing data of PTC and normal samples were used for screening differentially expressed (DE) microRNAs (DE‑miRNAs), long non‑coding RNAs (DE‑lncRNAs) and genes (DEGs). Subsequently, lncRNA‑miRNA, miRNA‑gene (that is, miRNA‑mRNA) and gene‑gene interaction pairs were extracted and used to construct regulatory networks. Feature genes in the miRNA‑mRNA network were identified by topological analysis and recursive feature elimination analysis...
May 11, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29766597/a-functional-assay-for-the-clinical-annotation-of-genetic-variants-of-uncertain-significance-in-diamond-blackfan-anemia
#7
Anna Aspesi, Marta Betti, Marika Sculco, Chiara Actis, Cristina Olgasi, Marcin W Wlodarski, Adrianna Vlachos, Jeffrey M Lipton, Ugo Ramenghi, Claudio Santoro, Antonia Follenzi, Steven R Ellis, Irma Dianzani
Diamond-Blackfan anemia (DBA) is a rare genetic hypoplasia of erythroid progenitors characterized by mild to severe anemia and associated with congenital malformations. Clinical manifestations in DBA patients are quite variable and genetic testing has become a critical factor in establishing a diagnosis of DBA. The majority of DBA cases are due to heterozygous loss-of-function mutations in ribosomal protein (RP) genes. Causative mutations are fairly straightforward to identify in the case of large deletions and frameshift and nonsense mutations found early in a protein coding sequence, but diagnosis becomes more challenging in the case of missense mutations and small in-frame indels...
May 15, 2018: Human Mutation
https://www.readbyqxmd.com/read/29763967/machine-learning-algorithms-for-outcome-prediction-in-chemo-radiotherapy-an-empirical-comparison-of-classifiers
#8
Timo M Deist, Frank J W M Dankers, Gilmer Valdes, Robin Wijsman, I-Chow Hsu, Cary Oberije, Tim Lustberg, Johan van Soest, Frank Hoebers, Arthur Jochems, Issam El Naqa, Leonard Wee, Olivier Morin, David R Raleigh, Wouter Bots, Johannes H Kaanders, José Belderbos, Margriet Kwint, Timothy Solberg, René Monshouwer, Johan Bussink, Andre Dekker, Philippe Lambin
PURPOSE: Machine learning classification algorithms (classifiers) for prediction of treatment response are becoming more popular in radiotherapy literature. General machine learning literature provides evidence in favor of some classifier families (random forest, support vector machine, gradient boosting) in terms of classification performance. The purpose of this study is to compare such classifiers specifically for (chemo)radiotherapy datasets and to estimate their average discriminative performance for radiation treatment outcome prediction...
May 15, 2018: Medical Physics
https://www.readbyqxmd.com/read/29760686/the-transcriptional-regulator-tfb-rf1-activates-transcription-of-a-putative-abc-transporter-in-pyrococcus-furiosus
#9
Robert Reichelt, Katharina M A Ruperti, Martina Kreuzer, Stefan Dexl, Michael Thomm, Winfried Hausner
Transcription factor B recruiting factor 1 (TFB-RF1; PF1088) is a transcription regulator which activates transcription on archaeal promoters containing weak TFB recognition elements (BRE) by recruiting TFB to the promoter. The mechanism of activation is described in detail, but nothing is known about the biological function of this protein in Pyrococcus furiosus . The protein is located in an operon structure together with the hypothetical gene pf1089 and western blot as well as end-point RT-PCR experiments revealed an extremely low expression rate of both proteins...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29757733/object-classification-with-joint-projection-and-low-rank-dictionary-learning
#10
Homa Foroughi, Nilanjan Ray, Hong Zhang
For an object classification system, the most critical obstacles toward real-world applications are often caused by large intra-class variability, arising from different lightings, occlusion, and corruption, in limited sample sets. Most methods in the literature would fail when the training samples are heavily occluded, corrupted or have significant illumination or viewpoint variations. Besides, most of the existing methods and especially deep learning-based methods, need large training sets to achieve a satisfactory recognition performance...
February 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/29754237/crispr-cas9-mediated-genome-editing-and-transcriptional-control-in-yarrowia-lipolytica
#11
Cory Schwartz, Ian Wheeldon
The discovery and adaptation of RNA-guided nucleases has resulted in the rapid development of efficient, scalable, and easily accessible synthetic biology tools for targeted genome editing and transcriptional control. In these systems, for example CRISPR-Cas9 from Streptococcus pyogenes, a protein with nuclease activity is targeted to a specific nucleotide sequence by a short RNA molecule, whereupon binding it cleaves the targeted nucleotide strand. To extend this genome-editing ability to the industrially important oleaginous yeast Yarrowia lipolytica, we developed a set of easily usable and effective CRISPR-Cas9 episomal vectors...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29753757/dpp-pseaac-a-dna-binding-protein-prediction-model-using-chou-s-general-pseaac
#12
M Saifur Rahman, Swakkhar Shatabda, Sanjay Saha, M Kaykobad, M Sohel Rahman
A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting whether a protein can bind with a DNA or not. In this paper, we focus on building a new computational model to identify DNA-BPs in an efficient and accurate way. Our model extracts meaningful information directly from the protein sequences, without any dependence on functional domain or structural information...
May 10, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29743670/vector-based-navigation-using-grid-like-representations-in-artificial-agents
#13
Andrea Banino, Caswell Barry, Benigno Uria, Charles Blundell, Timothy Lillicrap, Piotr Mirowski, Alexander Pritzel, Martin J Chadwick, Thomas Degris, Joseph Modayil, Greg Wayne, Hubert Soyer, Fabio Viola, Brian Zhang, Ross Goroshin, Neil Rabinowitz, Razvan Pascanu, Charlie Beattie, Stig Petersen, Amir Sadik, Stephen Gaffney, Helen King, Koray Kavukcuoglu, Demis Hassabis, Raia Hadsell, Dharshan Kumaran
Deep neural networks have achieved impressive successes in fields ranging from object recognition to complex games such as Go1,2 . Navigation, however, remains a substantial challenge for artificial agents, with deep neural networks trained by reinforcement learning3-5 failing to rival the proficiency of mammalian spatial behaviour, which is underpinned by grid cells in the entorhinal cortex 6 . Grid cells are thought to provide a multi-scale periodic representation that functions as a metric for coding space7,8 and is critical for integrating self-motion (path integration)6,7,9 and planning direct trajectories to goals (vector-based navigation)7,10,11 ...
May 9, 2018: Nature
https://www.readbyqxmd.com/read/29741719/xispec-web-based-visualization-analysis-and-sharing-of-proteomics-data
#14
Lars Kolbowski, Colin Combe, Juri Rappsilber
We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts...
May 8, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29741583/lzw-kernel-fast-kernel-utilizing-variable-length-code-blocks-from-lzw-compressors-for-protein-sequence-classification
#15
Gleb Filatov, Bruno Bauwens, Attila Kertész-Farkas
Motivation: Bioinformatics studies often rely on similarity measures between sequence pairs, which often pose a bottleneck in large-scale sequence analysis. Results: Here, we present a new convolutional kernel function for protein sequences called the LZW-Kernel. It is based on code words identified with the Lempel-Ziv-Welch (LZW) universal text compressor. The LZW-Kernel is an alignment-free method, it is always symmetric, is positive, always provides 1.0 for self-similarity and it can directly be used with Support Vector Machines (SVMs) in classification problems, contrary to normalized compression distance (NCD), which often violates the distance metric properties in practice and requires further techniques to be used with SVMs...
May 7, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29738863/porcine-igf1-synonymous-mutation-alter-gene-expression-and-protein-binding-affinity-with-igf1r
#16
Yunyun Cheng, Songcai Liu, Gang Wang, Wenzhen Wei, Shan Huang, Rui Yang, Hongwei Geng, Haoyang Li, Jie Song, Lidan Sun, Hao Yu, Linlin Hao
CONTEXT: Insulin like growth factor 1 (IGF1) is privotal in the regulation of animal growth and is a single-chain globular protein composed of B, C, A, and D regions, of which the C region is involved in maintaining high affinity binding to the IGF1 receptor (IGF1R). PURPOSE: In this study, significant expression differences between large pigs and miniature pigs were detected and only one synonymous SNP (c.258G>A) in the C region of the coding sequence of IGF1 gene was screened...
May 5, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29720246/rapid-identification-of-medically-important-mosquitoes-by-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry
#17
Abhishek Mewara, Megha Sharma, Taruna Kaura, Kamran Zaman, Rakesh Yadav, Rakesh Sehgal
BACKGROUND: Accurate and rapid identification of dipteran vectors is integral for entomological surveys and is a vital component of control programs for mosquito-borne diseases. Conventionally, morphological features are used for mosquito identification, which suffer from biological and geographical variations and lack of standardization. We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for protein profiling of mosquito species from North India with the aim of creating a MALDI-TOF MS database and evaluating it...
May 2, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29718113/prediction-of-lncrna-disease-associations-based-on-inductive-matrix-completion
#18
Chengqian Lu, Mengyun Yang, Feng Luo, Fang-Xiang Wu, Min Li, Yi Pan, Yaohang Li, Jianxin Wang
Motivation: Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. Mutations and dysregulations of lncRNAs are implicated in miscellaneous human diseases. Predicting lncRNA-disease associations is beneficial to disease diagnosis as well as treatment. Although many computational methods have been developed, precisely identifying lncRNA-disease associations, especially for novel lncRNAs, remains challenging. Results: In this study, we propose a method (named SIMCLDA) for predicting potential lncRNA-disease associations based on inductive matrix completion...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29716060/improving-performance-of-differential-pulse-coding-modulation-based-digital-mobile-fronthaul-employing-noise-shaping
#19
Haibo Li, Xiang Li, Ming Luo
A differential pulse coding modulation with noise shaping (NS-DPCM) is proposed to achieve better error vector magnitude (EVM) performance in a digital mobile fronthaul. Compared to previous DPCM based digital mobile fronthaul, a feedback loop combined with a finite-impulse-response (FIR) filter is added to the quantizer of DPCM encoder to operate as a quantization noise shaping technique block. The noise shaping technique increases the signal-to-quantization noise ratio by reshaping the spectrum of the quantization noise...
April 30, 2018: Optics Express
https://www.readbyqxmd.com/read/29715911/variability-of-the-reflectance-coefficient-of-skylight-from-the-ocean-surface-and-its-implications-to-ocean-color
#20
Alexander Gilerson, Carlos Carrizo, Robert Foster, Tristan Harmel
The value and spectral dependence of the reflectance coefficient (ρ) of skylight from wind-roughened ocean surfaces is critical for determining accurate water leaving radiance and remote sensing reflectances from shipborne, AERONET-Ocean Color and satellite observations. Using a vector radiative transfer code, spectra of the reflectance coefficient and corresponding radiances near the ocean surface and at the top of the atmosphere (TOA) are simulated for a broad range of parameters including flat and windy ocean surfaces with wind speeds up to 15 m/s, aerosol optical thicknesses of 0-1 at 440nm, wavelengths of 400-900 nm, and variable Sun and viewing zenith angles...
April 16, 2018: Optics Express
keyword
keyword
112492
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"