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Ontology

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https://www.readbyqxmd.com/read/28087900/itraq-based-quantitative-proteomic-analysis-and-bioinformatics-study-of-proteins-in-pterygia
#1
Dandan Linghu, Lili Guo, Yinghua Zhao, Zhiming Liu, Mingwei Zhao, Lvzhen Huang, Xiaoxin Li
PURPOSE: To analysis proteins in the tissue of pterygia, and to investigate their potential roles in pterygia, using the comparative proteomic technique of Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) coupled with offline 2DLC-MS/MS, Western-bolt. METHOD: The tissues of pterygia and healthy conjunctiva were collected from 10 pterygia patients (6 females, 4 males; average age was 52 years old; average course of disease was 6 years) in our hospital from September, 2015 to March, 2016...
January 13, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28087837/off-target-effects-of-neuroleptics-and-antidepressants-on-saccharomyces-cerevisiae
#2
M Caldara, S Graziano, M Gullì, S Cadonici, Nelson Marmiroli
Over the past years, the use of antidepressants and neuroleptics has steadily increased. Although incredibly useful to treat disorders like depression, schizophrenia, epilepsy, or mental retardation, these drugs display many side effects. Toxicogenomic studies aim to limit this problem by trying to identify cellular targets and off-targets of medical compounds. The baker yeast Saccharomyces cerevisiae has been shown to be a key player in this approach, as it represents an incredible toolbox for the dissection of complex biological processes...
January 13, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28087174/hgdb-a-web-retrieving-cardiovascular-associated-gene-data
#3
Faezeh Noorabad-Ghahroodi, Samaneh Abdi, Amir Hossein Zand, Mohammad Najafi
BACKGROUND: The use of data obtained from high throughput techniques in genetics studies is an essential subject in biology. The system approaches of networking and enriching may improve the data management. Here, we annotated the molecular features for cardiovascular-associated genes and presented the HGDB search-based database (www.hgdb.ir). METHODS: The initial seed data was primarily used from Gene Ontology and was automatically enriched with other molecular features...
January 5, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28086873/cecal-micrornaome-response-to-salmonella-enterica-serovar-enteritidis-infection-in-white-leghorn-layer
#4
Guixian Wu, Yukai Qi, Xiaoyi Liu, Ning Yang, Guiyun Xu, Liying Liu, Xianyao Li
BACKGROUND: Salmonella enterica serovar Enteritidis (SE) is a food-borne pathogen and of great threat to human health through consuming the contaminated poultry products. MicroRNAs (miRNAs) play an important role in different biological activities and have been shown to regulate the innate immunity in the bacterial infection. The objective of this study is to identify miRNAs associated with SE infection in laying chicken cecum. RESULTS: Average number of reads of three libraries constructed from infected and non-infected chickens was 12,476,156 and 10,866,976, respectively...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086788/comprehensive-circrna-expression-profile-and-selection-of-key-circrnas-during-priming-phase-of-rat-liver-regeneration
#5
Lifei Li, Jianlin Guo, Yanhui Chen, Cuifang Chang, Cunshuan Xu
BACKGROUND: Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081235/comprehensive-rna-seq-profiling-to-evaluate-the-sheep-mammary-gland-transcriptome-in-response-to-experimental-mycoplasma-agalactiae-infection
#6
Rohini Chopra-Dewasthaly, Melanie Korb, René Brunthaler, Reinhard Ertl
Mycoplasma agalactiae is a worldwide serious pathogen of small ruminants that usually spreads through the mammary route causing acute to subacute mastitis progressing to chronic persistent disease that is hard to eradicate. Knowledge of mechanisms of its pathogenesis and persistence in the mammary gland are still insufficient, especially the host-pathogen interplay that enables it to reside in a chronic subclinical state. This study reports transcriptome profiling of mammary tissue from udders of sheep experimentally infected with M...
2017: PloS One
https://www.readbyqxmd.com/read/28079497/meanings-of-waves-electroencephalography-and-society-in-mexico-city-1940-1950
#7
Nuria Valverde Pérez
Argument This paper focuses on the uses of electroencephalograms (EEGs) in Mexico during their introductory decade from 1940 to 1950. Following Borck (2006), I argue that EEGs adapted to fit local circumstances and that this adjustment led to the consolidation of different ways of making science and the emergence of new objects of study and social types. I also maintain that the way EEGs were introduced into the institutional networks of Mexico entangled them in discussions about the objective and juridical definitions of social groups, thereby preempting concerns about their technical and epistemic limitations...
December 2016: Science in Context
https://www.readbyqxmd.com/read/28077914/modelling-expertise-at-different-levels-of-granularity-using-semantic-similarity-measures-in-the-context-of-collaborative-knowledge-curation-platforms
#8
Hasti Ziaimatin, Tudor Groza, Tania Tudorache, Jane Hunter
Collaboration platforms provide a dynamic environment where the content is subject to ongoing evolution through expert contributions. The knowledge embedded in such platforms is not static as it evolves through incremental refinements - or micro-contributions. Such refinements provide vast resources of tacit knowledge and experience. In our previous work, we proposed and evaluated a Semantic and Time-dependent Expertise Profiling (STEP) approach for capturing expertise from micro-contributions. In this paper we extend our investigation to structured micro-contributions that emerge from an ontology engineering environment, such as the one built for developing the International Classification of Diseases (ICD) revision 11...
December 2016: Journal of Intelligent Information Systems
https://www.readbyqxmd.com/read/28077568/automatic-query-generation-using-word-embeddings-for-retrieving-passages-describing-experimental-methods
#9
Ferhat Aydın, Zehra Melce Hüsünbeyi, Arzucan Özgür
Information regarding the physical interactions among proteins is crucial, since protein-protein interactions (PPIs) are central for many biological processes. The experimental techniques used to verify PPIs are vital for characterizing and assessing the reliability of the identified PPIs. A lot of information about PPIs and the experimental methods are only available in the text of the scientific publications that report them. In this study, we approach the problem of identifying passages with experimental methods for physical interactions between proteins as an information retrieval search task...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077071/an-integrated-analysis-of-qtl-mapping-and-rna-sequencing-provides-further-insights-and-promising-candidates-for-pod-number-variation-in-rapeseed-brassica-napus-l
#10
Jiang Ye, Yuhua Yang, Bo Chen, Jiaqin Shi, Meizhong Luo, Jiepeng Zhan, Xinfa Wang, Guihua Liu, Hanzhong Wang
BACKGROUND: As the most important yield component in rapeseed (Brassica napus L.), pod number is determined by a series of successive growth and development processes. Pod number shows extensive variation in rapeseed natural germplasm, which is valuable for genetic improvement. However, the genetic and especially the molecular mechanism for this kind of variation are poorly understood. In this study, we conducted QTL mapping and RNA sequencing, respectively, using the BnaZNRIL population and its two parental cultivars Zhongshuang11 and No...
January 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28075478/high-expression-of-rab43-predicts-poor-prognosis-and-is-associated-with-epithelial-mesenchymal-transition-in-gliomas
#11
Ming-Zhi Han, Bin Huang, An-Jing Chen, Xin Zhang, Ran Xu, Jian Wang, Xin-Gang Li
The Ras-related GTP-binding protein (RAB) family plays an important role in regulating signal transduction and cellular processes including vesicle transport, cytoskeleton formation and membrane trafficking. More recently, several RAB members have been reported to promote tumorigenesis in many types of cancers. However, the clinical significance and potential function of RAB43 in gliomas remain unclear. Herein, we found that RAB43 was upregulated and positively correlated with the grade of progression in glioma patients by in silico analysis and immunohistochemistry (IHC)...
January 3, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28075450/integrated-analysis-of-differentially-expressed-genes-and-pathways-in-triple%C3%A2-negative-breast-cancer
#12
Cancan Peng, Wenli Ma, Wei Xia, Wenling Zheng
Triple‑negative breast cancer (TNBC) is a heterogeneous disease characterized by an aggressive phenotype and reduced survival. The aim of the present study was to investigate the molecular mechanisms involved in the carcinogenesis of TNBC and to identify novel target molecules for therapy. The differentially expressed genes (DEGs) in TNBC and normal adjacent tissue were assessed by analyzing the GSE41970 microarray data using Qlucore Omics Explorer, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes...
January 4, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28074419/deciphering-the-molecular-mechanisms-involved-in-hiv-associated-lipoatrophy-by-transcriptomics-a-pilot-study
#13
Patricia Pérez-Matute, María Iñiguez, Emma Recio-Fernández, José-Antonio Oteo
HIV-associated lipoatrophy (LA) has considerable implications for risk of metabolic diseases, quality of life, and adherence to treatments. Although it has decreased in high-income countries, it is still very common in resource-limited countries. Understanding the pathophysiological mechanisms of LA can open the possibility to explore new ways to treat or prevent this condition. To identify new markers for an accurate and quick diagnosis will be also of interest. Thus, we aimed to examine functional classes of genes implicated in LA and to identify potential new markers for an accurate/quick diagnosis of LA and future complications...
January 10, 2017: Journal of Physiology and Biochemistry
https://www.readbyqxmd.com/read/28071676/transcriptome-analysis-of-neo-tetraploid-rice-reveals-specific-differential-gene-expressions-associated-with-fertility-and-heterosis
#14
Haibin Guo, Jean Nestor Mendrikahy, Lei Xie, Junfeng Deng, Zijun Lu, Jinwen Wu, Xiang Li, Muhammad Qasim Shahid, Xiangdong Liu
Polyploid rice hybrids have a powerful biological and yield potential that may become a new way for rice breeding; however, low fertility is major hindrance in commercial utilization. Here, we developed a neo-tetraploid rice that could overcome the sterility of autotetraploid rice and produce high heterosis. Transcriptome analysis of F1 hybrid developed by crossing neo-tetraploid with autotetraploid rice displayed 807, 663 and 866 differentially expressed genes that uniquely associated with F1 and specific to (DEGFu-sp) anther, ovary and leaf, respectively...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28069692/genes-involved-in-development-and-differentiation-are-commonly-methylated-in-cancers-derived-from-multiple-organs-a-single-institutional-methylome-analysis-using-1007-tissue-specimens
#15
Kentaro Ohara, Eri Arai, Yoriko Takahashi, Nanako Ito, Ayako Shibuya, Koji Tsuta, Ryoji Kushima, Hitoshi Tsuda, Hidenori Ojima, Hiroyuki Fujimoto, Shun-Ichi Watanabe, Hitoshi Katai, Takayuki Kinoshita, Tatsuhiro Shibata, Takashi Kohno, Yae Kanai
The aim of this study was to clarify the significance of DNA methylation alterations shared by cancers derived from multiple organs. We analyzed single-institutional methylome data by single-CpG-resolution Infinium assay for 1,007 samples of non-cancerous tissue (N) and corresponding cancerous tissue (T) obtained from lung, stomach, kidney, breast and liver. Principal component analysis revealed that N samples of each organ showed distinct DNA methylation profiles, DNA methylation profiles of N samples of each organ being inherited by the corresponding T samples and DNA methylation profiles of T samples being more similar to those of N samples in the same organ than those of T samples in other organs...
January 9, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28069422/identification-of-ecdysteroid-receptor-mediated-signaling-pathways-in-the-hepatopancreas-of-the-red-swamp-crayfish-procambarus-clarkii
#16
Baojian Zhu, Lin Tang, Yingying Yu, Huimin Yu, Lei Wang, Cen Qian, Guoqing Wei, Chaoliang Liu
The hepatopancreas of crustaceans plays an important role in lipid and carbohydrate metabolism, digestion of food, and biogenesis. In this study, the hepatopancreas transcriptome from the red crayfish Procambarus clarkii was characterized for the first time using high-throughput sequencing, producing approximately 41.4 million reads were obtained. After de novo assembly, 57,363 unigenes with an average length of 725bp were identified, Gene Ontology analysis categorized 22,580 as being involved in biological processes, among which metabolic process and cellular process groups were the most highly enriched...
January 6, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28069052/toward-a-comprehensive-drug-ontology-extraction-of-drug-indication-relations-from-diverse-information-sources
#17
Mark E Sharp
BACKGROUND: Drug ontologies could help pharmaceutical researchers overcome information overload and speed the pace of drug discovery, thus benefiting the industry and patients alike. Drug-disease relations, specifically drug-indication relations, are a prime candidate for representation in ontologies. There is a wealth of available drug-indication information, but structuring and integrating it is challenging. RESULTS: We created a drug-indication database (DID) of data from 12 openly available, commercially available, and proprietary information sources, integrated by terminological normalization to UMLS and other authorities...
January 10, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28068976/il-1%C3%AE-induced-modulation-of-gene-expression-profile-in-human-dermal-fibroblasts-the-effects-of-thai-herbal-sahatsatara-formula-piperine-and-gallic-acid-possessing-antioxidant-properties
#18
Onusa Thamsermsang, Pravit Akarasereenont, Tawee Laohapand, Uraiwan Panich
BACKGROUND: Pain is the main symptom of most musculoskeletal disorders and can be caused by inflammation in association with oxidative stress. Thai herbal Sahatsatara formula (STF), a polyherbal formula, has been traditionally used for relieving muscle pain and limb numbness. This study aimed to investigate biologically active compounds of STF and its pharmacological effects related to antioxidant and anti-inflammatory activities. METHODS: The identification of possibly active compounds of STF was performed by high performance liquid chromatography (HPLC)...
January 10, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28068923/domestication-of-rice-has-reduced-the-occurrence-of-transposable-elements-within-gene-coding-regions
#19
Xukai Li, Kai Guo, Xiaobo Zhu, Peng Chen, Ying Li, Guosheng Xie, Lingqiang Wang, Yanting Wang, Staffan Persson, Liangcai Peng
BACKGROUND: Transposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are thus proposed as an ideal model to study TEs roles in the context of plant genome evolution. As TEs may contribute to improved rice growth and grain quality, it is of pivotal significance for worldwide food security and biomass production. RESULTS: We analyzed three cultivated rice species and their closest five wild relatives for distribution and content of TEs in their genomes...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068916/inferring-condition-specific-targets-of-human-tf-tf-complexes-using-chip-seq-data
#20
Chia-Chun Yang, Min-Hsuan Chen, Sheng-Yi Lin, Erik H Andrews, Chao Cheng, Chun-Chi Liu, Jeremy J W Chen
BACKGROUND: Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mammalian two-hybrid experiments or data mining. Lately, a wealth of ChIP-seq data on human TFs under different experiment conditions are available, making it possible to investigate condition-specific (cell type and/or physiologic state) TF complexes and their target genes...
January 10, 2017: BMC Genomics
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