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https://www.readbyqxmd.com/read/29036784/decreased-expression-of-lncrna-vps9d1-as1-in-gastric-cancer-and-its-clinical-significance
#1
Min Chen, Xiaoliang Wu, Wenjuan Ma, Qianghua Zhou, Xing Wang, Rongxin Zhang, Jiahong Wang, Xianzi Yang
BACKGROUND: A recent study has demonstrated that the long non-coding RNA VPS9D1-AS1 is highly expressed in colorectal cancer and predicts poor prognosis. However, role of VPS9D1-AS1 in gastric cancer remained poorly understood. OBJECTIVE: The aim of this study is to decipher the expression of VPS9D1-AS1 in gastric cancer (GC) patients, so as to assess whether or not it could be used as a novel biomarker for prognosis in gastric cancer patients. METHODS: The expression of VPS9D1-AS1 was examined in cancer tissues and paired adjacent non-tumorous tissues from 126 gastric cancer patients using qRT-PCR...
September 29, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/29036709/deep-learning-of-the-splicing-epi-genetic-code-reveals-a-novel-candidate-mechanism-linking-histone-modifications-to-esc-fate-decision
#2
Yungang Xu, Yongcui Wang, Jiesi Luo, Weiling Zhao, Xiaobo Zhou
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036692/clinical-utility-of-texture-analysis-of-18f-fdg-pet-ct-in-patients-with-stage-i-lung-cancer-treated-with-stereotactic-body-radiotherapy
#3
Kazuya Takeda, Kentaro Takanami, Yuko Shirata, Takaya Yamamoto, Noriyoshi Takahashi, Kengo Ito, Kei Takase, Keiichi Jingu
We evaluated the reproducibility and predictive value of texture parameters and existing parameters of 18F-FDG PET/CT images in Stage I non-small-cell lung cancer (NSCLC) patients treated with stereotactic body radiotherapy (SBRT). Twenty-six patients with Stage I NSCLC (T1-2N0M0) were retrospectively analyzed. All of the patients underwent an 18F-FDG PET/CT scan before treatment and were treated with SBRT. Each tumor was delineated using PET Edge (MIM Software Inc., Cleveland, OH), and texture parameters were calculated using open-source code CGITA...
September 21, 2017: Journal of Radiation Research
https://www.readbyqxmd.com/read/29036653/mircarta-a-central-repository-for-collecting-mirna-candidates
#4
Christina Backes, Tobias Fehlmann, Fabian Kern, Tim Kehl, Hans-Peter Lenhof, Eckart Meese, Andreas Keller
The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036616/deeploc-prediction-of-protein-subcellular-localization-using-deep-learning
#5
José Juan Almagro Armenteros, Casper Kaae Sønderby, Søren Kaae Sønderby, Henrik Nielsen, Ole Winther
Motivation: The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036481/identification-of-the-direct-regulon-of-ntca-during-early-acclimation-to-nitrogen-starvation-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#6
Joaquín Giner-Lamia, Rocío Robles-Rengel, Miguel A Hernández-Prieto, M Isabel Muro-Pastor, Francisco J Florencio, Matthias E Futschik
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036445/development-validation-and-demonstration-of-the-nthu-flight-dose-calculator
#7
An-Lun Li, Wei-Fan Pan, Rong-Jiun Sheu
Galactic cosmic-ray-induced air showers constitute the largest source of radiation exposure for aircrew and passengers. To facilitate the evaluation of effective doses received by this population, a database containing dose rates of various radiation components in the atmosphere was established; the parameterization accounted for altitude, geomagnetic rigidity and solar modulation. Energy spectra of secondary cosmic rays and effective dose rates were calculated using the FLUKA Monte Carlo code. An auxiliary MATLAB program with a graphical user interface was developed to estimate the aviation route dose through interpolation and integration...
September 23, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/29036429/genome-re-annotation-of-the-wild-strawberry-fragaria-vesca-using-extensive-illumina-and-smrt-based-rna-seq-datasets
#8
Yongping Li, Wei Wei, Jia Feng, Huifeng Luo, Mengting Pi, Zhongchi Liu, Chunying Kang
The genome of the wild diploid strawberry species Fragaria vesca, an ideal model system of cultivated strawberry (Fragaria × ananassa, octoploid) and other Rosaceae family crops, was first published in 2011 and followed by a new assembly (Fvb). However, the annotation for Fvb mainly relied on ab initio predictions and included only predicted coding sequences, therefore an improved annotation is highly desirable. Here, a new annotation version named v2.0.a2 was created for the Fvb genome by a pipeline utilizing one PacBio library, 90 Illumina RNA-seq libraries, and 9 small RNA-seq libraries...
September 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29036404/the-value-of-prior-knowledge-in-machine-learning-of-complex-network-systems
#9
Dana Ferranti, David Krane, David Craft
Motivation: Our overall goal is to develop machine-learning approaches based on genomics and other relevant accessible information for use in predicting how a patient will respond to a given proposed drug or treatment. Given the complexity of this problem, we begin by developing, testing and analyzing learning methods using data from simulated systems, which allows us access to a known ground truth. We examine the benefits of using prior system knowledge and investigate how learning accuracy depends on various system parameters as well as the amount of training data available...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036354/plncpro-for-prediction-of-long-non-coding-rnas-lncrnas-in-plants-and-its-application-for-discovery-of-abiotic-stress-responsive-lncrnas-in-rice-and-chickpea
#10
Urminder Singh, Niraj Khemka, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Long non-coding RNAs (lncRNAs) make up a significant portion of non-coding RNAs and are involved in a variety of biological processes. Accurate identification/annotation of lncRNAs is the primary step for gaining deeper insights into their functions. In this study, we report a novel tool, PLncPRO, for prediction of lncRNAs in plants using transcriptome data. PLncPRO is based on machine learning and uses random forest algorithm to classify coding and long non-coding transcripts. PLncPRO has better prediction accuracy as compared to other existing tools and is particularly well-suited for plants...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036274/a-robust-df-reml-framework-for-variance-components-estimation-in-genetic-studies
#11
V M Lourenço, P C Rodrigues, A M Pires, H-P Piepho
Motivation: In genetic association studies, linear mixed models (LMMs) are used to test for associations between phenotypes and candidate single nucleotide polymorphisms (SNPs). These same models are also used to estimate heritability, which is central not only to evolutionary biology but also to the prediction of the response to selection in plant and animal breeding, as well as the prediction of disease risk in humans. However, when one or more of the underlying assumptions are violated, the estimation of variance components may be compromised and therefore so may the estimates of heritability and any other functions of these...
July 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036205/characterization-of-micrornas-of-beta-macrocarpa-and-their-responses-to-beet-necrotic-yellow-vein-virus-infection
#12
Jun-Ying Liu, Hui-Yan Fan, Ying Wang, Yong-Liang Zhang, Da-Wei Li, Jia-Lin Yu, Cheng-Gui Han
Plant microRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development, defense, and symptom development. Here, 547 known miRNAs representing 129 miRNA families, and 282 potential novel miRNAs were identified in Beta macrocarpa using small RNA deep sequencing. A phylogenetic analysis was performed, and 8 Beta lineage-specific miRNAs were identified. Through a differential expression analysis, miRNAs associated with Beet necrotic yellow vein virus (BNYVV) infection were identified and confirmed using a microarray analysis and stem-loop RT-qPCR...
2017: PloS One
https://www.readbyqxmd.com/read/29036195/mutational-and-large-deletion-study-of-genes-implicated-in-hereditary-forms-of-primary-hyperparathyroidism-and-correlation-with-clinical-features
#13
Elena Pardi, Simona Borsari, Federica Saponaro, Fausto Bogazzi, Claudio Urbani, Stefano Mariotti, Francesca Pigliaru, Chiara Satta, Fabiana Pani, Gabriele Materazzi, Paolo Miccoli, Lorena Grantaliano, Claudio Marcocci, Filomena Cetani
The aim of this study was to carry out genetic screening of the MEN1, CDKN1B and AIP genes, both by direct sequencing of the coding region and multiplex ligation-dependent probe amplification (MLPA) assay in the largest monocentric series of Italian patients with Multiple Endocrine Neoplasia type 1 syndrome (MEN1) and Familial Isolated Hyperparathyroidism (FIHP). The study also aimed to describe and compare the clinical features of MEN1 mutation-negative and mutation-positive patients during long-term follow-up and to correlate the specific types and locations of MEN1 gene mutations with onset and aggressiveness of the main MEN1 manifestations...
2017: PloS One
https://www.readbyqxmd.com/read/29035779/data-driven-heterogeneity-in-mathematical-learning-disabilities-based-on-the-triple-code-model
#14
Christian Peake, Juan E Jiménez, Cristina Rodríguez
Many classifications of heterogeneity in mathematical learning disabilities (MLD) have been proposed over the past four decades, however no empirical research has been conducted until recently, and none of the classifications are derived from Triple Code Model (TCM) postulates. The TCM proposes MLD as a heterogeneous disorder, with two distinguishable profiles: a representational subtype and a verbal subtype. A sample of elementary school 3rd to 6th graders was divided into two age cohorts (3rd - 4th grades, and 5th - 6th grades)...
October 13, 2017: Research in Developmental Disabilities
https://www.readbyqxmd.com/read/29035718/assessment-of-the-coding-accuracy-of-warfarin-related-bleeding-events
#15
Thomas Delate, Aubrey E Jones, Nathan P Clark, Daniel M Witt
INTRODUCTION: Using International Classification of Diseases, 9th edition (ICD-9) diagnosis codes to identify potential warfarin-related bleeding events from administrative datasets is highly efficient but may be prone to identifying non-events. The objective of this study was to evaluate the ability of bleeding-related ICD-9 codes to identify true bleeding events in patients who were receiving warfarin therapy at the time of hospitalization. METHODS: This was a cross-sectional study conducted in an integrated healthcare delivery system...
October 12, 2017: Thrombosis Research
https://www.readbyqxmd.com/read/29035682/the-role-of-mir319a-and-its-target-gene-tcp4-in-the-regulation-of-pistil-development-in-prunus-mume
#16
Wanxu Wang, Ting Shi, Xiaopeng Ni, Yanshuai Xu, Shenchun Qu, Zhihong Gao
The microRNAs (miRNAs) comprise a broad class of non-coding small endogenous RNAs that are associated with many biological processes through the regulation of target genes, such as leaf morphogenesis and polarity, biotic and abiotic stress responses, root and flower development. We identified a miRNA that affects flower development, miR319a, in Prunus mume. The Pm-miR319a target, Pm-TCP4, was validated by 5'RACE. The higher expression of Pm-TCP4 in imperfect flowers showed that the Pm-TCP4 might promote pistil abortion...
October 16, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29035203/developing-a-nonstationary-computational-framework-with-application-to-modeling-dynamic-modulations-in-neural-spiking-responses
#17
Amir Akbarian, Kaiser Niknam, Mohammadbagher Parsa, Kelsey Clark, Behrad Noudoost, Neda Nategh
OBJECTIVE: This paper aims to develop a computational model that incorporates the functional effects of modulatory covariates (such as context, task, or behavior), which dynamically alter the relationship between the stimulus and the neural response. METHODS: We develop a general computational approach along with an efficient estimation procedure in the widely used generalized linear model (GLM) framework to characterize such nonstationary dynamics in spiking response and spatiotemporal characteristics of a neuron at the level of individual trials...
October 13, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/29034127/socio-demographic-factors-which-significantly-relate-to-the-prediction-of-burns-severity-in-children
#18
Khalid Alnababtah, Salim Khan
BACKGROUND: Burns are considered one of the biggest wounds and the most devastating injuries humans can receive as they have prolonged consequences which are not only physical, but psychological in addition to the cost of treatment. The aim of the study was to explore the relationships between socio-demographic factors (SDF) and the incidence and mechanisms of burn injuries in children. The objectives were to identify the multiple and various factors responsible for the occurrence of significant burns in children; to explore and investigate the relationship between these factors; to critically analyse SDF on the incidence and mechanisms of burns and to develop a contextual model with a view to informing future health care policy and health promotion programmes...
2017: International Journal of Burns and Trauma
https://www.readbyqxmd.com/read/29033926/micrornas-in-taenia-solium-neurocysticercosis-insights-as-promising-agents-in-host-parasite-interaction-and-their-potential-as-biomarkers
#19
REVIEW
Renzo Gutierrez-Loli, Miguel A Orrego, Oscar G Sevillano-Quispe, Luis Herrera-Arrasco, Cristina Guerra-Giraldez
MicroRNAs (miRNAs) are short, endogenous, non-coding, single-stranded RNAs involved in post-transcriptional gene regulation. Although, several miRNAs have been identified in parasitic helminths, there is little information about their identification and function in Taenia. Furthermore, the impact of miRNAs in neurocysticercosis, the brain infection caused by larvae of Taenia solium is still unknown. During chronic infection, T. solium may activate numerous mechanisms aimed to modulate host immune responses...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29032608/microrna-profiling-reveals-dysregulated-micrornas-and-their-target-gene-regulatory-networks-in-cemento-ossifying-fibroma
#20
Thaís Dos Santos Fontes Pereira, João Artur Ricieri Brito, André Luiz Sena Guimarães, Carolina Cavaliéri Gomes, Júlio Cesar Tanos de Lacerda, Wagner Henriques de Castro, Roney Santos Coimbra, Marina Gonçalves Diniz, Ricardo Santiago Gomez
BACKGROUND: Cemento-ossifying fibroma (COF) is a benign fibro-osseous neoplasm of uncertain pathogenesis and its treatment results morbidity. MicroRNAs (miRNA) are small non-coding RNAs that regulate gene expression and may represent therapeutic targets. The purpose of the study was to generate a comprehensive miRNA profile of COF compared to normal bone. Additionally, the most relevant pathways and target genes of differentially expressed miRNA were investigated by in silico analysis...
October 15, 2017: Journal of Oral Pathology & Medicine
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