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https://www.readbyqxmd.com/read/28454467/investigation-of-differentially-expressed-micrornas-and-genes-in-cervical-cancer-using-an-integrated-bioinformatics-analysis
#1
Zhanzhan Xu, Yu Zhou, Fang Shi, Yexuan Cao, Thi Lan Anh Dinh, Jing Wan, Min Zhao
Cervical cancer is one of the most common types of cancer among women worldwide. In order to identify the microRNAs (miRNAs/miRs) and mRNAs associated with the carcinogenesis of cervical cancer, and to investigate the molecular mechanisms of cervical cancer, an miRNA microarray, GSE30656, and 3 mRNA microarrays, GSE63514, GSE39001 and GSE9750, for cervical cancer were retrieved from Gene Expression Omnibus. These datasets were analyzed in order to obtain differentially-expressed genes (DEGs) and miRNAs using the GEO2R tool...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454466/identification-of-molecular-characteristics-induced-by-radiotherapy-in-rectal-cancer-based-on-microarray-data
#2
Chang Ge, Mengxia Wu, Guifang Chen, Guanying Yu, Dehui Ji, Shaozhao Wang
The present study aimed to reveal the molecular characteristics induced by radiotherapy in rectal cancer at the transcriptome level. Microarray data (ID, GSE26027) downloaded from the Gene Expression Omnibus database were re-analyzed to identify differentially expressed genes (DEGs) between rectal cancer tissues during and prior to radiotherapy. The DEGs were then inputted into the database for annotation, visualization and integrated discovery, an online tool to perform enrichment analyses, and into the search tool for the retrieval of interacting genes/proteins database to identify protein-protein interactions (PPIs)...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454465/microarray-based-analysis-of-gene-regulation-by-mesenchymal-stem-cells-in-breast-cancer
#3
Ming Zhang, Chang E Gao, Wen Hui Li, Yi Yang, Li Chang, Jian Dong, Yan Xin Ren, De Dian Chen
Breast cancer is one of the most common malignant tumors with a high case-fatality rate among women. The present study aimed to investigate the effects of mesenchymal stem cells (MSCs) on breast cancer by exploring the potential underlying molecular mechanisms. The expression profile of GSE43306, which refers to MDA-MB-231 cells with or without a 1:1 ratio of MSCs, was downloaded from Gene Expression Omnibus database for differentially expressed gene (DEG) screening. The Database for Annotation, Visualization and Integrated Discovery was used for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454442/identification-of-target-genes-of-cediranib-in-alveolar-soft-part-sarcoma-using-a-gene-microarray
#4
Wenhua Jiang, Pengfei Liu, Xiaodong Li, Ping Wang
The aim of the present study was to identify the target genes of cediranib and the associated signaling pathways in alveolar soft part sarcoma (ASPS). A microarray dataset (GSE32569) was obtained from the Gene Expression Omnibus database. The R software package was used for data normalization and screening of differentially expressed genes (DEGs). The Database for Annotation, Visualization and Integrated Discovery was used to perform Gene Ontology analysis. Gene Set Enrichment Analysis was performed to obtain the up- and downregulated pathways in ASPS...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454367/matrix-metalloproteinases-in-vietnamese-patients-with-colorectal-cancer
#5
Thao Phuong Bui, Anh Ngoc Hoang, Phuong Lan Le, Bich Thi Pham, Linh Thi Tu Nguyen, Ha Minh Do, To Van Ta, Thai Hong Trinh
Matrix metalloproteinases (MMPs), a family of endopeptidases also known as gelatinases, have been reported to affect the acquisition of the cell proliferative, cell invasive and metastatic phenotype of several types of cancer. In particular, the gelatinases MMP-2 and -9 have been revealed to facilitate tumor growth and invasion in patients with colorectal cancer (CRC). However, it is not known whether the gelatinase activity of MMP-2 and -9 is also elevated in Vietnamese patients with CRC. The activity of MMP-2 and -9 in the tissue samples of 103 patients with CRC was evaluated by gelatin zymography and quantified using ImageJ...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454286/suspected-tumor-to-meningioma-metastasis-a-case-report
#6
Iuri Santana Neville, Davi Fontoura Solla, Arthur Maynart Oliveira, Cesar Casarolli, Manoel Jacobsen Teixeira, Wellingson Silva Paiva
Tumor-to-meningioma metastasis (TMM) is a fairly uncommon phenomenon. Only 7 cases of prostate cancer with TMM have previously been described in the literature. The present study aimed to report a case of prostate cancer TMM, and to discuss the relevant clinical and neuroimaging aspects of this condition. A 68-year-old patient presented with headaches, poor visual acuity in the left eye and ipsilateral eyelid droop 3 years after a Simpson II resection of a left sphenoid wing meningioma. Computed tomography revealed a hyperdense area suggestive of a recurrent left sphenoid wing meningioma...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454187/combination-of-transforaminal-and-interlaminar-percutaneous-endoscopic-lumbar-diskectomy-for-extensive-down-migrated-disk-herniation
#7
Kyung-Chul Choi, Jung Hyun Lee, Jin-Sung Kim, Dong Chan Lee, Choon Keun Park
Background and Study Aims The technique and instrumentation of percutaneous endoscopic lumbar diskectomy (PELD) have significantly improved. Thus its indications have been gradually expanding. Down-migrated disk, in particular, is regarded inaccessible by rigid instrumentation due to poor visualization and limited accessibility. We introduce a combination of transforaminal and interlaminar PELD for extensive down-migrated disk herniation at the L4-L5 level. Patients and Methods In the first case, a 48-year-old man had left L5 radicular pain...
April 28, 2017: Journal of Neurological Surgery. Part A, Central European Neurosurgery
https://www.readbyqxmd.com/read/28454106/different-patterns-of-age-related-central-olfactory-decline-in-men-and-women-as-quantified-by-olfactory-fmri
#8
Brittany Martinez, Prasanna Karunanayaka, Jianli Wang, Michael J Tobia, Megha Vasavada, Paul J Eslinger, Qing X Yang
Age-related olfactory decline, or presbyosmia, is a prevalent condition with potentially devastating consequences on both quality of life and safety. Despite clear evidence for this decline, it is unknown whether presbyosmia is sex-dependent and also whether it is due to central or peripheral olfactory system deterioration. Therefore, the goals of this study were to investigate the neurofunctional substrate of olfactory decline and examine its relationship to age and sex in thirty-seven (18 women, 19 men) healthy older participants using olfactory functional MRI (fMRI)...
April 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28454072/fluorescent-coumarin-based-probe-for-cysteine-and-homocysteine-with-live-cell-application
#9
Ling-Fang Wei, Natesan Thirumalaivasan, Yu-Cheng Liao, Shu-Pao Wu
Cysteine (Cys) and homocysteine (Hcy) are two of important biological thiols and function as important roles in several biological processes. The development of Cys and Hcy probes will help to explore the functions of biothiols in biological systems. In this work, a new coumarin-based probe AC, containing an acryloyl moiety, was developed for Cys and Hcy detection in cells. Cys and Hcy undergo a nucleophilic addition and subsequent cyclization reaction to remove to the acryloyl group and yield a fluorescent product, 7-hydroxylcomuarin...
April 20, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28453952/where-is-the-locus-of-the-lowercase-advantage-during-sentence-reading
#10
Manuel Perea, Eva Rosa, Ana Marcet
While most models of visual word identification and reading posit that a word's visual codes are rapidly transformed onto case-invariant representations (i.e., table and TABLE would equally activate the word unit corresponding to "table"), a number of experiments have shown a lowercase advantage in various word identification and reading tasks. In the present experiment, we examined the locus of this lowercase advantage by comparing the pattern of eye movements when reading sentences in lowercase vs. uppercase...
April 25, 2017: Acta Psychologica
https://www.readbyqxmd.com/read/28453888/live-imaging-of-extracellular-signal-regulated-kinase-and-protein-kinase-a-activities-during-thrombus-formation-in-mice-expressing-biosensors-based-on-f%C3%A3-rster-resonance-energy-transfer
#11
Takuya Hiratsuka, Takeshi Sano, Hisashi Kato, Naoki Komatsu, Masamichi Imajo, Yuji Kamioka, Kenta Sumiyama, Fumiaki Banno, Toshiyuki Miyata, Michiyuki Matsuda
BACKGROUND: Dynamic features of thrombus formation have been visualized by conventional video wide field microscopy or confocal microscopy in live mouse. However, due to technical limitations precise spatiotemporal regulation of intracellular signaling molecule activities, which have been extensively studied in vitro, remains elusive in vivo. OBJECTIVES: By two-photon excitation microscopy of transgenic mice expressing Förster resonance energy transfer (FRET) biosensors for extracellular signal-regulated kinase (ERK) and protein kinase A (PKA), we visualized ERK and PKA activities during thrombus formation in laser-injured subcutaneous arterioles RESULTS: When a core of densely packed platelets was developed, ERK activity was increased from the basal region close to the injured arterioles...
April 28, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28453823/a-flowchart-for-building-evidence-based-care-bundles-in-intensive-care-based-on-a-systematic-review
#12
Marjon Borgert, Jan Binnekade, Frederique Paulus, Astrid Goossens, Dave Dongelmans
Purpose: The Institute for Healthcare Improvement is the founder of the care bundled approach and described the methods used on how to develop care bundles. However, other useful methods are published as well. In this systematic review, we identified what different methods were used to design care bundles in intensive care units. The results were used to build a comprehensive flowchart to guide through the care bundle design process. Data sources: Electronic databases were searched for eligible studies in PubMed, EMBASE and CINAHL from January 2001 to August 2014...
April 1, 2017: International Journal for Quality in Health Care
https://www.readbyqxmd.com/read/28453814/graphene-specimen-support-technique-for-low-voltage-stem-imaging
#13
Masao Yamashita, Matthew Ryan Leyden, Hidehito Adaniya, Martin Philip Cheung, Teruhisa Hirai, Yabing Qi, Tsumoru Shintake
The scanning transmission electron microscopy (STEM) mode of today's field emission scanning electron microscopes enables sub-nanometer resolution imaging. Graphene is a single-atom thick, electrically conductive material, making it an excellent specimen support for the low voltage STEM imaging of nanometer-sized objects such as viruses. Here we present low voltage STEM images of bacteriophage T4 recorded on highly cleaned graphene films. The results show that ultrathin graphene support films markedly improve image signal at low accelerating voltages...
April 27, 2017: Microscopy
https://www.readbyqxmd.com/read/28453794/blood-flow-competition-after-aortic-valve-bypass-an-evaluation-using-computational-fluid-dynamics
#14
Koji Kawahito, Naoyuki Kimura, Kenji Komiya, Masanori Nakamura, Yoshio Misawa
OBJECTIVES: Aortic valve bypass (AVB) (apico-aortic conduit) remains an effective surgical alternative for patients in whom surgical aortic valve replacement or transcatheter aortic valve implantation is not feasible. However, specific complications include thrombus formation, possibly caused by stagnation arising from flow competition between the antegrade and retrograde flow, but this has not been fully investigated. The aim of this study was to analyse flow characteristics after AVB and to elucidate mechanisms of intra-aortic thrombus using computational fluid dynamics (CFD)...
May 1, 2017: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/28453679/biopaxviz-a-cytoscape-application-for-the-visual-exploration-of-metabolic-pathway-evolution
#15
Fotis E Psomopoulos, Dimitrios M Vitsios, Shakuntala Baichoo, Christos A Ouzounis
Summary: BioPAXViz is a Cytoscape (version 3) application, providing a comprehensive framework for metabolic pathway visualization. Beyond the basic parsing, viewing and browsing roles, the main novel function that BioPAXViz provides is a visual comparative analysis of metabolic pathway topologies across pre-computed pathway phylogenomic profiles given a species phylogeny. Furthermore, BioPAXViz supports the display of hierarchical trees that allow efficient navigation through sets of variants of a single reference pathway...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453675/circosvcf-circos-visualization-of-whole-genome-sequence-variations-stored-in-vcf-files
#16
E Drori, D Levy, P Smirin-Yosef, O Rahimi, M Salmon-Divon
Summary: Visualization of whole-genomic variations in a meaningful manner assists researchers in gaining new insights into the underlying data, especially when it comes in the context of whole genome comparisons. CircosVCF is a web based visualization tool for genome-wide variant data described in VCF files, using circos plots. The user friendly interface of CircosVCF supports an interactive design of the circles in the plot, and the integration of additional information such as experimental data or annotations...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453672/primerize-2d-automated-primer-design-for-rna-multidimensional-chemical-mapping
#17
Siqi Tian, Rhiju Das
Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453667/linearity-of-network-proximity-measures-implications-for-set-based-queries-and-significance-testing
#18
Sean Maxwell, Mark R Chance, Mehmet Koyutürk
Motivation: In recent years, various network proximity measures have been proposed to facilitate the use of biomolecular interaction data in a broad range of applications. These applications include functional annotation, disease gene prioritization, comparative analysis of biological systems and prediction of new interactions. In such applications, a major task is the scoring or ranking of the nodes in the network in terms of their proximity to a given set of 'seed' nodes (e.g. a group of proteins that are identified to be associated with a disease, or are deferentially expressed in a certain condition)...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453644/traitrateprop-a-web-server-for-the-detection-of-trait-dependent-evolutionary-rate-shifts-in-sequence-sites
#19
Eli Levy Karin, Haim Ashkenazy, Susann Wicke, Tal Pupko, Itay Mayrose
Understanding species adaptation at the molecular level has been a central goal of evolutionary biology and genomics research. This important task becomes increasingly relevant with the constant rise in both genotypic and phenotypic data availabilities. The TraitRateProp web server offers a unique perspective into this task by allowing the detection of associations between sequence evolution rate and whole-organism phenotypes. By analyzing sequences and phenotypes of extant species in the context of their phylogeny, it identifies sequence sites in a gene/protein whose evolutionary rate is associated with shifts in the phenotype...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28453602/theory-of-mind-and-executive-functioning-following-stroke
#20
Jackie Hamilton, Bogna Radlak, Paul G Morris, Louise H Phillips
Objective: Cognitive deficits following stroke are well documented, but less is known about problems with social skills such as understanding others' thoughts and feelings. This study investigated the effect of stroke on a visual-affective measure of social understanding: the Reading the Mind in the Eyes test (RMET). The aims were to investigate whether right hemisphere stroke was particularly detrimental to this aspect of Theory of Mind (ToM), and investigate the relationship between ToM ability and executive function following stroke...
April 27, 2017: Archives of Clinical Neuropsychology: the Official Journal of the National Academy of Neuropsychologists
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