keyword
MENU ▼
Read by QxMD icon Read
search

Ontology

keyword
https://www.readbyqxmd.com/read/28938722/novel-transcriptome-resources-for-three-scleractinian-coral-species-from-the-indo-pacific
#1
Carly D Kenkel, Line K Bay
Transcriptomic resources for coral species can provide insight into coral evolutionary history and stress-response physiology. Goniopora columna, Galaxea astreata, and Galaxea acrhelia are scleractinian corals of the Indo-Pacific, representing a diversity of morphologies and life-history traits. G. columna and G. astreata are common and cosmopolitan, while G. acrhelia is largely restricted to the coral triangle and Great Barrier Reef. Reference transcriptomes for these species were assembled from replicate colony fragments exposed to elevated (31°C) and ambient (27°C) temperatures...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938573/iatc-mhyb-a-hybrid-multi-label-classifier-for-predicting-the-classification-of-anatomical-therapeutic-chemicals
#2
Xiang Cheng, Shu-Guang Zhao, Xuan Xiao, Kuo-Chen Chou
Recommended by the World Health Organization (WHO), drug compounds have been classified into 14 main ATC (Anatomical Therapeutic Chemical) classes according to their therapeutic and chemical characteristics. Given an uncharacterized compound, can we develop a computational method to fast identify which ATC class or classes it belongs to? The information thus obtained will timely help adjusting our focus and selection, significantly speeding up the drug development process. But this problem is by no means an easy one since some drug compounds may belong to two or more than two ATC classes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937906/protein-activation-in-periapical-reaction-to-iodoform-containing-root-canal-sealer
#3
Nili Tickotsky, Moti Moskovitz
OBJECTIVES: An association between root canal sealers and periapical lesions in primary dentition has been suggested, yet the chemical-protein interactions that may be involved in it have not been studied. The present study explored root sealer components' effect on periapical tissue proteins using bioinformatics tools. STUDY DESIGN: For each chemical component of Endoflas F.S. root sealing material we identified the known and predicted target proteins, using STITCH (search tool for interactions of chemicals http://stitch...
September 22, 2017: Journal of Clinical Pediatric Dentistry
https://www.readbyqxmd.com/read/28937590/logistic-model-to-support-service-modularity-for-the-promotion-of-reusability-in-a-web-objects-enabled-iot-environment
#4
Muhammad Golam Kibria, Sajjad Ali, Muhammad Aslam Jarwar, Sunil Kumar, Ilyoung Chong
Due to a very large number of connected virtual objects in the surrounding environment, intelligent service features in the Internet of Things requires the reuse of existing virtual objects and composite virtual objects. If a new virtual object is created for each new service request, then the number of virtual object would increase exponentially. The Web of Objects applies the principle of service modularity in terms of virtual objects and composite virtual objects. Service modularity is a key concept in the Web Objects-Enabled Internet of Things (IoT) environment which allows for the reuse of existing virtual objects and composite virtual objects in heterogeneous ontologies...
September 22, 2017: Sensors
https://www.readbyqxmd.com/read/28936926/revisiting-the-continuing-bonds-theory-the-cultural-uniqueness-of-the-bei-dao-phenomenon-in-taiwanese-widows-widowers
#5
Wan-Lin Lee, Yi-Chen Hou, Yaw-Sheng Lin
In the present study, we used the phenomenological approach to rediscover the ontological meaning of relationships with the deceased in Taiwanese widows/widowers. We first revised the original Western definitions of grief, bereavement, and mourning to fit Taiwanese culture. We used the word bei dao to indicate the mixed nature of grief and mourning in the Taiwanese bereavement process. Then we reanalyzed data from a previous study, which was conducted in 2006. In the previous qualitative research, each subject was interviewed 3 to 4 times in the mourning state over an 18-month interval that began at the point of the spouse's death...
October 2017: Qualitative Health Research
https://www.readbyqxmd.com/read/28936162/rna-sequencing-analysis-reveals-a-regulatory-role-for-transcription-factor-fezf2-in-the-mature-motor-cortex
#6
Alison J Clare, Hollie E Wicky, Ruth M Empson, Stephanie M Hughes
Forebrain embryonic zinc finger (Fezf2) encodes a transcription factor essential for the specification of layer 5 projection neurons (PNs) in the developing cerebral cortex. As with many developmental transcription factors, Fezf2 continues to be expressed into adulthood, suggesting it remains crucial to the maintenance of neuronal phenotypes. Despite the continued expression, a function has yet to be explored for Fezf2 in the PNs of the developed cortex. Here, we investigated the role of Fezf2 in mature neurons, using lentiviral-mediated delivery of a shRNA to conditionally knockdown the expression of Fezf2 in the mouse primary motor cortex (M1)...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28935818/increased-mir-124-3p-in-microglial-exosomes-following-traumatic-brain-injury-inhibits-neuronal-inflammation-and-contributes-to-neurite-outgrowth-via-their-transfer-into-neurons
#7
Shan Huang, Xintong Ge, Jinwen Yu, Zhaoli Han, Zhenyu Yin, Ying Li, Fanglian Chen, Haichen Wang, Jianning Zhang, Ping Lei
Neuronal inflammation is the characteristic pathologic change of acute neurologic impairment and chronic traumatic encephalopathy after traumatic brain injury (TBI). Inhibiting the excessive inflammatory response is essential for improving the neurologic outcome. To clarify the regulatory mechanism of microglial exosomes on neuronal inflammation in TBI, we focused on studying the impact of microglial exosomal miRNAs on injured neurons in this research. We used a repetitive (r)TBI mouse model and harvested the injured brain extracts from the acute to the chronic phase of TBI to treat cultured BV2 microglia in vitro The microglial exosomes were collected for miRNA microarray analysis, which showed that the expression level of miR-124-3p increased most apparently in the miRNAs...
September 21, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28934431/genetic-profiling-and-comorbidities-of-zika-infection
#8
Mohammad Ali Moni, Pietro Lio'
Background: The difficulty in distinguishing infection by Zika virus (ZIKV) from other flaviviruses is a global health concern, particularly given the high risk of neurologic complications (including Guillain-Barré syndrome [GBS]) with ZIKV infection. Methods: We developed quantitative frameworks to compare and explore infectome, diseasome, and comorbidity of ZIKV infections. We analyzed gene expression microarray and RNA-Seq data from ZIKV, West Nile fever (WNF), chikungunya, dengue, yellow fever, Japanese encephalitis virus, GBS, and control datasets...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934375/into-the-wild-parallel-transcriptomics-of-the-tsetse-wigglesworthia-mutualism-within-kenyan-populations
#9
Miguel Medina Munoz, Adam R Pollio, Hunter L White, Rita V M Rio
Tsetse flies (Diptera: Glossinidae) have medical significance as the obligate vectors of African trypanosomes. In addition, tsetse harbor a simple gut microbiota. A predominant gut microbiota member, the Gammaproteobacterium Wigglesworthia spp., has coevolved with tsetse for a significant portion of Glossina radiation proving critical to tsetse fitness. Although multiple roles have been described for Wigglesworthia within colony flies, little research has been dedicated towards functional characterization within wild tsetse...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28934298/transcriptome-analysis-of-callery-pear-pyrus-calleryana-reveals-a-comprehensive-signalling-network-in-response-to-alternaria-alternata
#10
Jialiang Kan, Tingli Liu, Na Ma, Hui Li, Xiaogang Li, Jinyan Wang, Baolong Zhang, Youhong Chang, Jing Lin
The pear is an important temperate fruit worldwide that is produced by a group of species in the genus Pyrus. Callery pear (Pyrus calleryana Decne) is characterized by high resistance to multiple diseases, good adaptability, and high ornamental value, and is therefore widely planted in pear orchards for edible fruit production or as stock. Plant pathogens are a major threat to pear yield. Black spot disease, caused by the filamentous fungus Alternaria alternata, is one of the most serious diseases in pear. Elucidation of resistant genes to black spot disease is extremely important for understanding the underlying mechanisms as well as for the development of resistant cultivars...
2017: PloS One
https://www.readbyqxmd.com/read/28934086/towards-ontology-based-decision-support-systems-for-complex-ultrasound-diagnosis-in-obstetrics-and-gynecology
#11
P Maurice, F Dhombres, E Blondiaux, S Friszer, L Guilbaud, N Lelong, B Khoshnood, J Charlet, N Perrot, E Jauniaux, D Jurkovic, J-M Jouannic
INTRODUCTION: We have developed a new knowledge base intelligent system for obstetrics and gynecology ultrasound imaging, based on an ontology and a reference image collection. This study evaluates the new system to support accurate annotations of ultrasound images. We have used the early ultrasound diagnosis of ectopic pregnancies as a model clinical issue. MATERIAL AND METHODS: The ectopic pregnancy ontology was derived from medical texts (4260 ultrasound reports of ectopic pregnancy from a specialist center in the UK and 2795 Pubmed abstracts indexed with the MeSH term "Pregnancy, Ectopic") and the reference image collection was built on a selection from 106 publications...
May 2017: Journal of gynecology obstetrics and human reproduction
https://www.readbyqxmd.com/read/28934029/comparative-proteomics-of-streptococcus-pneumoniae-response-to-vancomycin-treatment
#12
Xiao-Yan Yang, Jing-Yu Xu, Qiu-Xia Wei, Xuesong Sun, Qing-Yu He
Streptococcus pneumoniae is a gram-positive pathogen that causes otitis media, pneumonia, meningitis, and other serious diseases. Vancomycin is one of the most important drugs currently used for the treatment of gram-positive bacterial infections, representing, importantly, the last line of defense against bacteria that have developed resistance to other antibiotics. While primary efforts of most investigations focused on the antibacterial mechanism of vancomycin, few studies have been performed to assess the tolerance mechanism of bacteria to vancomycin...
September 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28933415/integrative-systems-biology-investigation-of-fabry-disease
#13
Marco Fernandes, Holger Husi
Fabry disease (FD) is a rare X-linked recessive genetic disorder caused by a deficient activity of the lysosomal enzyme alpha-galactosidase A (GLA) and is characterised by intra-lysosomal accumulation of globotriaosylceramide (Gb3). We performed a meta-analysis of peer-reviewed publications including high-throughput omics technologies including naïve patients and those undergoing enzyme replacement therapy (ERT). This study describes FD on a systems level using a systems biology approach, in which molecular data sourced from multi-omics studies is extracted from the literature and integrated as a whole in order to reveal the biochemical processes and molecular pathways potentially affected by the dysregulation of differentially expressed molecules...
November 15, 2016: Diseases (Basel)
https://www.readbyqxmd.com/read/28932774/transcriptomic-and-bioinformatics-analysis-of-the-early-time-course-of-the-response-to-prostaglandin-f2-alpha-in-the-bovine-corpus-luteum
#14
Heather Talbott, Xiaoying Hou, Fang Qiu, Pan Zhang, Chittibabu Guda, Fang Yu, Robert A Cushman, Jennifer R Wood, Cheng Wang, Andrea S Cupp, John S Davis
RNA expression analysis was performed on the corpus luteum tissue at five time points after prostaglandin F2 alpha treatment of midcycle cows using an Affymetrix Bovine Gene v1 Array. The normalized linear microarray data was uploaded to the NCBI GEO repository (GSE94069). Subsequent statistical analysis determined differentially expressed transcripts ± 1.5-fold change from saline control with P ≤ 0.05. Gene ontology of differentially expressed transcripts was annotated by DAVID and Panther. Physiological characteristics of the study animals are presented in a figure...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28931430/global-proteomic-profiling-of-yersinia-ruckeri-strains
#15
Gokhlesh Kumar, Karin Hummel, Timothy J Welch, Ebrahim Razzazi-Fazeli, Mansour El-Matbouli
Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM) of salmonids. There is little information regarding the proteomics of Y. ruckeri. Herein, we perform whole protein identification and quantification of biotype 1 and biotype 2 strains of Y. ruckeri grown under standard culture conditions using a shotgun proteomic approach. Proteins were extracted, digested and peptides were separated by a nano liquid chromatography system and analyzed with a high-resolution hybrid triple quadrupole time of flight mass spectrometer coupled via a nano ESI interface...
September 20, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28929028/fish-ontology-framework-for-taxonomy-based-fish-recognition
#16
Najib M Ali, Haris A Khan, Amy Y-Hui Then, Chong Ving Ching, Manas Gaur, Sarinder Kaur Dhillon
Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval...
2017: PeerJ
https://www.readbyqxmd.com/read/28928868/villi-specific-gene-expression-reveals-novel-prognostic-biomarkers-in-multiple-human-cancers
#17
Botao Zhang, Lin Feng, Honglin Guo, Hongxia Li, Yuanjing Wang, Kaitai Zhang, Xuexin Yu, Shujun Cheng
Despite many striking connections, the biological similarities between embryonic development and tumorigenesis have not been well explored. Development of the placental villi is a crucial process involving many cellular activities, including immunity, proliferation, and cell adhesion. In this study, we designed a strategy to identify the gene expression pattern of villi development and to explore the corresponding features in tumors. We discovered villi-specific genes that are highly expressed in the villus as opposed to the mature placenta and then measured the expression levels of these genes in tumors...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28928827/inhibition-of-c-myc-expression-accounts-for-an-increase-in-the-number-of-multinucleated-cells-in-human-cervical-epithelial-cells
#18
Feng Mei Cui, Xiu Jin Sun, Cheng Cheng Huang, Qiu Chen, Yong Ming He, Shi Meng Zhang, Hua Guan, Man Song, Ping Kun Zhou, Jun Hou
The present study aimed to explore the mechanisms by which c-Myc is involved in mitotic catastrophe. HeLa-630 is a cell line stably silenced for c-Myc expression that was established in the laboratory of the School of Radiation Medicine and Protection. Multinucleated cells were observed in this line, and gene expression analysis was utilized to examine differences in gene expression in these cells compared with in the control cells transfected with the control plasmid. Gene ontology analysis was performed for differentially expressed genes...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28928672/micrornas-clustered-within-the-14q32-locus-are-associated-with-endothelial-damage-and-microparticle-secretion-in-bicuspid-aortic-valve-disease
#19
Neus Martínez-Micaelo, Raúl Beltrán-Debón, Gerard Aragonés, Marta Faiges, Josep M Alegret
Background: We previously described that PECAM(+) circulating endothelial microparticles (EMPs) are elevated in bicuspid aortic valve (BAV) disease as a manifestation of endothelial damage. In this study, we hypothesized that this endothelial damage, is functionally related to the secretion of a specific pattern of EMP-associated miRNAs. Methods: We used a bioinformatics approach to correlate the PECAM(+) EMP levels with the miRNA expression profile in plasma in healthy individuals and BAV patients (n = 36)...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28928286/hpv-integration-in-hnscc-correlates-with-survival-outcomes-immune-response-signatures-and-candidate-drivers
#20
Lada A Koneva, Yanxiao Zhang, Shama Virani, Pelle B Hall, Jonathan B McHugh, Douglas B Chepeha, Gregory Wolf, Thomas E Carey, Laura S Rozek, Maureen A Sartor
The incidence of human papillomavirus (HPV)-related oropharynx cancer has steadily increased over the past two decades, and now represents a majority of oropharyngeal cancer cases. Integration of the HPV genome into the host genome is a common event during carcinogenesis that has clinically-relevant effects if the viral early genes are transcribed. Understanding the impact of HPV integration on clinical outcomes of head and neck squamous cell carcinoma (HNSCC) is critical for implementing de-escalated treatment approaches for HPV-positive HNSCC patients...
September 19, 2017: Molecular Cancer Research: MCR
keyword
keyword
4269
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"