5,986 Hits in 5.6 sec

Extracting Evidence Fragments for Distant Supervision of Molecular Interactions [article]

Gully A Burns, Pradeep Dasigi, Eduard H. Hovy
2017 bioRxiv   pre-print
Using figure codes as anchors, we linked evidence fragments to INTACT data records as an example of distant supervision so that we could use INTACT's preexisting, manually-curated structured interaction  ...  We describe a methodology for automatically extracting 'evidence fragments' from a set of biomedical experimental research articles.  ...  We thank Anita de Waard, Mihai Surdeanu, Clay Morrison, and Hans Chalupsky for their contributions.  ... 
doi:10.1101/192856 fatcat:dt5o2fmbjvgdjcuj7gzyg6ekzq

Extracting Protein-Reaction Information from Tables of Unpredictable Format and Content in the Molecular Biology Literature

Sam Sloate, Vincent Hsiao, Nina Charness, Ethan Lowman, Chris Maxey, Guannan Ren, Nathan Fields, Leora Morgenstern
2016 International Joint Conference on Artificial Intelligence  
This paper focuses on the specific problem of automated table reading (ATR): automating the interpretation and extraction of information from proteinreaction information (PRI) tables in the molecular biology  ...  literature (MBL), in the context of a general knowledge-based approach to automating table reading.We report on the results of our system evaluation, which demonstrated a precision of greater than .9  ...  We note that if successful, a rule-based system could be used to automate the finding and labeling of training data; that is, it would enable distant-supervision of learning.  ... 
dblp:conf/ijcai/SloateHCLMRFM16 fatcat:j66ezeojpvctlofop6r62ljrzq

The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex

Hung-Ta Chen, Linda Warfield, Steven Hahn
2007 Nature Structural & Molecular Biology  
Elucidating these molecular interactions within the transcription machinery is important for understanding the functional roles of the general transcription factors and the mechanisms of transcription  ...  interactions.  ...  ACKNOWLEDGEMENTS We thank Gail Miller, Beth Moorefield, Neeman Mohibullah, Ted Young, and other members of the Hahn lab for their comments and suggestions throughout the course of this work. We thank  ... 
doi:10.1038/nsmb1272 pmid:17632521 pmcid:PMC2483787 fatcat:3iu53kh265efvmykaewhvptqyu

Identification of mycorrhizal fungi from single pelotons ofDactylorhiza majalis(Orchidaceae) using single-strand conformation polymorphism and mitochondrial ribosomal large subunit DNA sequences

K. A. kristiansen, D. L. taylor, R. kjøller, H. N. rasmussen, S. rosendahl
2001 Molecular Ecology  
The gene was amplified using DNA extracted from single pelotons obtained from fresh and silica gel dried roots.  ...  Furthermore, sequencing a variety of well-characterized orchid isolates expanded the fungal database of the mitochondrial ribosomal LsDNA.  ...  Acknowledgements We thank Charlotte Hansen and Kenn Kristiansen for help in the laboratory, and David Hibbett for two Tulasnella DNA samples.  ... 
doi:10.1046/j.0962-1083.2001.01324.x pmid:11555252 fatcat:h54stawtyjcwjbw3cr4x7gwndu

Optimal Response in a Patient With CML Expressing BCR–ABL1 E6A2 Fusion Transcript With Nilotinib Therapy: A Case Report

2020 In Vivo  
The use of primers recognizing more distant exons from the common BCR-ABL1 breakpoint region correctly identified the atypical BCR-ABL1 e16a2 fusion transcript.  ...  front-line second-generation tyrosine kinase inhibitors for this genotype.  ...  Molecular analysis showed no amplification of specific products with primers for the detection of the BCR-ABL1 canonical fusion transcripts e13a2, e14a2 and e1a2.  ... 
doi:10.21873/invivo.11933 pmid:32354950 pmcid:PMC7279803 fatcat:sg76kap5xnh5pn2lxq6oiapqzy

OUP accepted manuscript

2018 Database: The Journal of Biological Databases and Curation  
We present Reach, a system for automated, large-scale machine reading of biomedical papers that can extract mechanistic descriptions of biological processes with relatively high precision at high throughput  ...  We demonstrate that combining the extracted pathway fragments with existing biological data analysis algorithms that rely on curated models helps identify and explain a large number of previously unidentified  ...  We are especially grateful to Tonia Korves and Lynette Hirschman for making these results available before their publication, and for the many clarification discussions.  ... 
doi:10.1093/database/bay098 fatcat:xpnrphqq6jgsbeuafu5pogr2uq

Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives

Jia Xu, Pengwei Yang, Shang Xue, Bhuvan Sharma, Marta Sanchez-Martin, Fang Wang, Kirk A. Beaty, Elinor Dehan, Baiju Parikh
2019 Human Genetics  
In this paper, we review the current status and future directions of AI application in cancer genomics within the context of workflows to integrate genomic analysis for precision cancer care.  ...  Publicly available tools or algorithms for key NLP technologies in the literature mining for evidencebased clinical recommendations are reviewed and compared.  ...  Entity extraction Bio-NER is the foundation of evidence extraction for precision medicine.  ... 
doi:10.1007/s00439-019-01970-5 fatcat:qkcyzmq4ina5jg4ieyqktjblte

Effect of the Andean Geography and Climate on the Specialized Metabolism of Its Vegetation: The Subtribe Espeletiinae (Asteraceae) as a Case Example

Guillermo F. Padilla-González, Mauricio Diazgranados, Fernando B. Da Costa
2021 Metabolites  
However, the influence of Andean geography and climate as drivers of metabolic variation in Andean plants is poorly elucidated.  ...  Here, we studied the influence of those factors on the metabolome of the subtribe Espeletiinae (Asteraceae) using liquid chromatography coupled to high-resolution mass spectrometry data of over two hundred  ...  Sadgrove (Royal Botanic Gardens, Kew, UK) for proofreading and comments on the manuscript. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/metabo11040220 pmid:33916648 pmcid:PMC8065660 fatcat:nxrb2zoc5jbzljiocktaslgaza

A Ribonucleoprotein Supercomplex Involved intrans-Splicing of Organelle Group II Introns

Olga Reifschneider, Christina Marx, Jessica Jacobs, Laxmikanth Kollipara, Albert Sickmann, Dirk Wolters, Ulrich Kück
2016 Journal of Biological Chemistry  
Here, we address the question whether fragmentation of trans-acting RNAs is accompanied by the formation of a chloroplast spliceosome-like machinery.  ...  Using a combination of liquid chromatographymass spectrometry (LC-MS), size exclusion chromatography, and quantitative RT-PCR, we provide the first characterization of a high molecular weight ribonucleoprotein  ...  Acknowledgments-We thank Katja Schmitt, Ivonne Schelberg, and Ingeborg Godehardt for excellent technical assistance.  ... 
doi:10.1074/jbc.m116.750570 pmid:27645995 pmcid:PMC5087748 fatcat:ozx7jupsq5gwxbgjcm2ddqhteu

Insights into the Influence of Specific Splicing Events on the Structural Organization of LRRK2

Dimitrios Vlachakis, Nikolaos Labrou, Costas Iliopoulos, John Hardy, Patrick Lewis, Hardy Rideout, Daniah Trabzuni
2018 International Journal of Molecular Sciences  
Previous human expression studies showed evidence of mRNA expression and splicing patterns that may contribute to our understanding of the function of LRRK2.  ...  Our molecular modelling study suggests that splicing events in the ROC/COR domains will have major consequences on the enzymatic function and dimer formation of LRRK2.  ...  Conflicts of Interest: The authors have no potential conflicting financial, personal or professional interests.  ... 
doi:10.3390/ijms19092784 pmid:30223621 pmcid:PMC6165039 fatcat:mjaxtwbwmfhtjbzjyiwo5mfzoi

Natural Ecosystem Surrounding a Conventional Banana Crop Improves Plant Health and Fruit Quality

Florence P. Castelan, Victor C. Castro-Alves, Lorenzo A. Saraiva, Talita P. Nascimento, Maria F. N. S. Cálhau, Carlos T. S. Dias, Beatriz R. Cordenunsi-Lysenko
2018 Frontiers in Plant Science  
In this "proof of principle" study, an innovative approach isolated natural biodiversity as the only variable between two banana crop areas, highlighting biodiversity benefits on crop health and fruit  ...  Tania Shiga, and Elias Araújo for their technical support, Dr. José Ozinaldo Alves de Sena and his team for analyzing soil and plant nutrition, Ms. Fabio Tomas for biodiversity assessment, and Dr.  ...  Hasime Tokeshi for their valuable advice. We also thank Chico from the COOPERAGUA -Guapiruvu community for his assistance in locating the experimental areas.  ... 
doi:10.3389/fpls.2018.00759 pmid:29930565 pmcid:PMC6001115 fatcat:cbrz5v4nrnbpvgumehlbzhmll4

Enhanced detection of cell-free DNA (cfDNA) enables its use as a reliable biomarker for diagnosis and prognosis of gastric cancer

Jiyoon Bu, Tae Hee Lee, Woo-jin Jeong, Michael J. Poellmann, Kara Mudd, Hyuk Soo Eun, Elizabeth W. Liu, Seungpyo Hong, Sung Hee Hyun, Jeffrey Chalmers
2020 PLoS ONE  
PDA-silica hybrids incorporated different molecular interactions to a single system, enhancing cfDNA capture by 1.34-fold compared to the conventional silica-based approach (p = 0.001), which was confirmed  ...  Among the cancer patients, plasma cfDNA levels exhibited a good correlation with the size of a tumor. cfDNA was also predicative of distant metastasis, as the median cfDNA levels of metastatic cancer patients  ...  surface, due to its strong adhesion with silica [14] ; and (2) Cooperation of different molecular interactions to a single system (i.e. combined interaction of PDA-nucleobases and silica-phosphate backones  ... 
doi:10.1371/journal.pone.0242145 pmid:33264292 fatcat:h3nztoo7trgfpgnbs3dnvsrwmi

High Expression of a tRNAPro Derivative Associates with Poor Survival and Independently Predicts Colorectal Cancer Recurrence

Panagiotis Tsiakanikas, Panagiotis G. Adamopoulos, Dimitra Tsirba, Pinelopi I. Artemaki, Iordanis N. Papadopoulos, Christos K. Kontos, Andreas Scorilas
2022 Biomedicines  
For this purpose, total RNA was extracted from 155 malignant colorectal tumors and 74 adjacent non-cancerous tissue specimens, polyadenylated and reverse-transcribed using an oligo-dT adapter as primer  ...  Fragments of tRNAPro are conserved among vertebrates, characterized by pleiotropic regulatory functions and have been found to discriminate colorectal tumors from normal colorectal mucosa.  ...  Acknowledgments: The research presented was carried out within the framework of a Stavros Niarchos Foundation grant to the National and Kapodistrian University of Athens (Grant ID 16785).  ... 
doi:10.3390/biomedicines10051120 pmid:35625858 pmcid:PMC9138872 fatcat:pk5zsmgowrc5zfahfzk2mw5nnm

Screening effective differential expression genes for hepatic carcinoma with metastasis in the peripheral blood mononuclear cells by RNA-seq

Yanting Shen, Lu Bu, Rui Li, Zhenzhu Chen, Fei Tian, Na Lu, Qinyu Ge, Yunfei Bai, Zuhong Lu
2017 OncoTarget  
In conclusions, CCL3, CCL3L1, JUN, IL8, and IL1B have the potential to be considered as candidates for future molecular diagnosis of the hepatic carcinoma with metastasis.  ...  The aim of this study was to use RNA-seq to screen the effective differential expression genes in the peripheral blood mononuclear cells for the hepatic carcinoma with metastasis.  ...  They have the potential to be considered as candidates for future molecular diagnosis of the hepatic carcinoma with metastasis.  ... 
doi:10.18632/oncotarget.15855 pmid:28427195 pmcid:PMC5438623 fatcat:fcw4m2hjszdlbko35ddsnebsgq

Typical Lung Carcinoids with Metastasis: Potential Role of MicroRNAs in the Regulation of Adaptive Immunity Associated with Disease: a Case Study

Ana L Seneda, Rainer M Lopez Lapa, Tainara F Felix, Iael W Minutentag, Carolina F Campos, Rogério A de Oliveira, Cristiano C Oliveira, Érica N Hasimoto, Daniele C Cataneo, Antonio J M Cataneo, Julio De Faveri, Sandra A Drigo (+2 others)
2021 Cellular Physiology and Biochemistry  
Identified miRNAs and target genes are potential candidates for validation in a larger number of cases.  ...  Molecular features of lung carcinoids have been poorly defined. microRNAs (miRNAs) are potent gene expression regulators with important roles in cancer development and progression.  ...  Reis: study design, data interpretation, study supervision, funding, manuscript writing.  ... 
doi:10.33594/000000320 pmid:33398982 fatcat:b5ku24p7nvaajeqr5i2bjatcly
« Previous Showing results 1 — 15 out of 5,986 results