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Ontology-based Extraction of Structured Information from Publications on Preclinical Experiments for Spinal Cord Injury Treatments

Benjamin Paassen, Andreas Stöckel, Raphael Dickfelder, Jan Philip Göpfert, Nicole Brazda, Tarek Kirchhoffer, Hans Werner Müller, Roman Klinger, Matthias Hartung, Philipp Cimiano
2014 Proceedings of the Third Workshop on Semantic Web and Information Extraction  
In this paper, we describe a first prototype of an ontology-based information extraction system that automatically extracts relevant preclinical knowledge about spinal cord injury treatments from natural  ...  Preclinical research in the field of central nervous system trauma advances at a fast pace, currently yielding over 8,000 new publications per year, at an exponentially growing rate.  ...  Related Work Our workflow for acquiring structured information in the domain of spinal cord injury treatments is an example of ontology-based information extraction systems (Wimalasuriya and Dou, 2010  ... 
doi:10.3115/v1/w14-6204 dblp:conf/acl-swaie/PaassenSDGBKMKH14 fatcat:n7e2hvzgyffqfcxcjuhrukhcb4

SCIE: Information Extraction for Spinal Cord Injury Preclinical Experiments - A Webservice and Open Source Toolkit [article]

Andreas Stöckel, Benjamin Paassen, Raphael Dickfelder, Jan Philip Göpfert, Nicole Brazda, Hans Werner Müller, Philipp Cimiano, Matthias Hartung, Roman Klinger
2015 bioRxiv   pre-print
We present SCIE, an automated information extraction pipeline capable of detecting relevant information in SCI publications based on ontological entity and probabilistic relation detection.  ...  Translational neuroscience in the field of spinal cord injuries (SCI) faces a strong disproportion between immense preclinical research efforts and a lack of therapeutic approaches successful in human  ...  Acknowledgement Roman Klinger has been partially funded by the "It's OWL" project ("Intelligent Technical Systems Ostwestfalen-Lippe"), a leading-edge technology and research cluster funded by German Ministry of  ... 
doi:10.1101/013458 fatcat:anwb6icsqjgn3jlzjx33thm2ri

Developing a data sharing community for spinal cord injury research

Alison Callahan, Kim D. Anderson, Michael S. Beattie, John L. Bixby, Adam R. Ferguson, Karim Fouad, Lyn B. Jakeman, Jessica L. Nielson, Phillip G. Popovich, Jan M. Schwab, Vance P. Lemmon
2017 Experimental Neurology  
with the Open Data Commons for Spinal Cord Injury (ODC-SCI) titled "Preclinical SCI Data: Creating a FAIR Share Community".  ...  The spinal cord injury (SCI) research field has a long history of collaborative initiatives that include sharing of preclinical research models and outcome measures.  ...  Acknowledgements The FAIR Share workshop was co-sponsored by the NINDS and the University of Alberta, with contributions from the International Spinal Research Trust (ISRT) (RES0034012), (KF), the Rick  ... 
doi:10.1016/j.expneurol.2017.05.012 pmid:28576567 fatcat:7dcdaqkgy5gy5nalab5sy245ea

Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury

Jordan W Squair, Seth Tigchelaar, Kyung-Mee Moon, Jie Liu, Wolfram Tetzlaff, Brian K Kwon, Andrei V Krassioukov, Christopher R West, Leonard J Foster, Michael A Skinnider
2018 eLife  
Spinal cord injury (SCI) is a devastating neurological condition for which there are currently no effective treatment options to restore function.  ...  Here, we describe a systems biology approach to integrate decades of small-scale experiments with unbiased, genome-wide gene expression from the human spinal cord, revealing a gene regulatory network signature  ...  Acknowledgments We thank Erin Erskine for assistance with animal experiments and Dr.  ... 
doi:10.7554/elife.39188 pmid:30277459 pmcid:PMC6173583 fatcat:ncpc4fa2ebar3hgdlmketw7bgq

Identification of Pharmacological Targets in Amyotrophic Lateral Sclerosis Through Genomic Analysis of Deregulated Genes and Pathways

Sabrina Paratore, Salvatore Pezzino, Sebastiano Cavallaro
2012 Current Genomics  
Riluzole is currently the only FDA approved drug for ALS, but it has only modest effects on survival. The majority of ALS cases are sporadic and probably associated to a multifactorial etiology.  ...  The present review will illustrate how the identification, prioritization and validation of preclinical therapeutics can be achieved through genomic analysis of critical pathways and networks deregulated  ...  ACKNOWLEDGEMENT The authors gratefully acknowledge Paolo Cantaro and Ambrogio Mazzeo for their encouragement, support and inspiration.  ... 
doi:10.2174/138920212800793366 pmid:23204922 pmcid:PMC3394120 fatcat:kuzoc22ohvctxd7fnipcoyujje

Gene Transcript Alterations in the Spinal Cord, Anterior Cingulate Cortex, and Amygdala in Mice Following Peripheral Nerve Injury

Songxue Su, Mengqi Li, Di Wu, Jing Cao, Xiuhua Ren, Yuan-Xiang Tao, Weidong Zang
2021 Frontiers in Cell and Developmental Biology  
Moreover, the comparisons of pain-, anxiety-, and depression-related DEGs among three regions present a particular molecular map among the spinal cord and supraspinal structures and indicate the region-dependent  ...  Our study provides a resource for gene transcript expression patterns in three distinct pain-related regions after peripheral nerve injury.  ...  The spinal cord is responsible for receiving information from nociceptors and projecting to the brain and plays a major role in integrating and modulating nociceptive signals (Kuner, 2010) .  ... 
doi:10.3389/fcell.2021.634810 pmid:33898422 pmcid:PMC8059771 fatcat:vwzb7vbai5cxfmwqkxyajmmkfy

Histaminergic transmission slows progression of amyotrophic lateral sclerosis

Savina Apolloni, Susanna Amadio, Paola Fabbrizio, Giovanna Morello, Antonio Gianmaria Spampinato, Emanuele Claudio Latagliata, Illari Salvatori, Daisy Proietti, Alberto Ferri, Luca Madaro, Stefano Puglisi‐Allegra, Sebastiano Cavallaro (+1 others)
2019 Journal of Cachexia, Sarcopenia and Muscle  
We identified 13 histamine-related genes deregulated in the spinal cord of two ALS patient subgroups, among which genes involved in histamine metabolism, receptors, transport, and secretion.  ...  from disease pathological signs.  ...  Acknowledgements The authors certify that they comply with the ethical guidelines for authorship and publishing of the Journal of Cachexia, Sarcopenia and Muscle. 48 Conflict of interest  ... 
doi:10.1002/jcsm.12422 pmid:31020811 pmcid:PMC6711424 fatcat:abo75ohkfbes3kwz55sfa44ijy

ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials

Kirill Borziak, Irena Parvanova, Joseph Finkelstein
2021 Database: The Journal of Biological Databases and Curation  
Our testing demonstrated the robustness of the proposed platform, by seamlessly harmonizing diverse common data elements, and the potential of this platform for driving knowledge generation from the aggregation  ...  Abstract Recent regenerative medicine studies have emphasized the need for increased standardization, harmonization and sharing of information related to stem cell product characterization, to help drive  ...  cord injury, spinal muscular atrophy with respiratory distress type 1, stroke, traumatic brain injury and type IV congenital dyserythropoietic anaemia.  ... 
doi:10.1093/database/baab038 pmid:34156448 fatcat:it6qn3ktbrc7pj6zhpsuvif7ge

Epigenetic inhibitor zebularine activates ear pinna wound closure in the mouse

Piotr Sass, Paweł Sosnowski, Justyna Podolak-Popinigis, Bartosz Górnikiewicz, Jolanta Kamińska, Milena Deptuła, Ewa Nowicka, Anna Wardowska, Jarosław Ruczyński, Piotr Rekowski, Piotr Rogujski, Natalia Filipowicz (+10 others)
2019 EBioMedicine  
Most studies on regenerative medicine focus on cell-based therapies and transplantations.  ...  a novel pharmacological strategy for regeneration.  ...  Acknowledgements This study was conducted within the "REGENNOVA" project on novel technologies for pharmacological stimulation of regeneration under the "STRATEGMED" program of the National Centre for  ... 
doi:10.1016/j.ebiom.2019.07.010 pmid:31303499 pmcid:PMC6710911 fatcat:nlvwshzpwraxblnvp6tttcqzo4

Transcriptomics Analysis of Porcine Caudal Dorsal Root Ganglia in Tail Amputated Pigs Shows Long-Term Effects on Many Pain-Associated Genes

Dale A. Sandercock, Mark W. Barnett, Jennifer E. Coe, Alison C. Downing, Ajit J. Nirmal, Pierpaolo Di Giminiani, Sandra A. Edwards, Tom C. Freeman
2019 Frontiers in Veterinary Science  
Microarrays were used to analyse whole DRG transcriptomes from tail amputated and sham-treated pigs 1, 8, and 16 weeks following tail treatment at either 3 or 63 days of age (8 pigs/treatment/age/time  ...  The aim of this study was to investigate the short- and long-term effects of tail amputation in pigs on caudal DRG gene expression at different stages of development, particularly in relation to genes  ...  ACKNOWLEDGMENTS The authors would like to thank the Cockle Park technical team, especially Mark Brett, Emma Malcolm, and Louisa Craigs for their help with pig management and procedures.  ... 
doi:10.3389/fvets.2019.00314 pmid:31620455 pmcid:PMC6760028 fatcat:y626jdoigrbw3gxwe37c7hpiui

Stem cells: sources and therapies

Manuela Monti, Cesare Perotti, Claudia Del Fante, Marila Cervio, Carlo Alberto Redi
2012 Biological Research  
therapies for regenerative medicine.  ...  The induction of cell pluripotency and the different stem cells sources are presented (embryonic, adult and cord blood).  ...  Helmut Zacharias for the time spent to critically read a preliminary version of the manuscript and for long discussions that definitely improved the paper significantly.  ... 
doi:10.4067/s0716-97602012000300002 pmid:23283430 fatcat:rr6kluarxbdc7gxuxa5qc6e3jm

Oral Presentations

2017 Global Spine Journal  
Microscopy was performed on equipment supported by the Microscopy Imaging Center (MIC), University of Bern, Switzerland. This project was supported by the Gebert Rüf Foundation project # GRS-X028/13.  ...  We thank Eva Roth for her help in IVD isolation and biomechanical assays.  ...  Ahmed 1 , Rizwan Akram 1 Background: The prognosis for spinal cord injuries varies depending on the severity of the injury.  ... 
doi:10.1177/2192568217708577 fatcat:xa6fqbninffwvpdylyble6wo74

Data sharing in psychology

Maryann E. Martone, Alexander Garcia-Castro, Gary R. VandenBos
2018 American Psychologist  
We draw on experiences in other domains to discuss attitudes towards data sharing, cost-benefits, best practices and infrastructure.  ...  Moreover, although not all issues around how and what to share have been resolved, a consensus on principles and best practices for effective data sharing and the infrastructure for sharing many types  ...  Jessica Nielson and Adam Ferguson for their helpful comments. AGC acknowledges the KOPAR, H2020-MSCA-IF-2014, Grant Agreement Number 655009.  ... 
doi:10.1037/amp0000242 pmid:29481105 pmcid:PMC5920518 fatcat:jeqjyeb3jfcvtkafq7tsa7uilq

Spared Nerve Injury Causes Sexually Dimorphic Mechanical Allodynia and Differential Gene Expression in Spinal Cords and Dorsal Root Ganglia in Rats

F.H.G. Ahlström, K. Mätlik, H. Viisanen, K.J. Blomqvist, X. Liu, T.O. Lilius, Y. Sidorova, E.A. Kalso, P.V. Rauhala
2021 Molecular Neurobiology  
Ipsilateral lumbar dorsal root ganglia (DRG) and spinal cord (SC) segments were collected for RNA-seq analysis with DESeq2 on Day 7.  ...  Cerebrospinal fluid (CSF) samples for proteomic analysis and DRGs and SCs for analysis of IB-4 and CGRP, and IBA1 and GFAP, respectively, were collected on Day 21.  ...  Acknowledgements Sini Miettinen is acknowledged for her expert work with the proteomics of the CSF.  ... 
doi:10.1007/s12035-021-02447-1 pmid:34331199 pmcid:PMC8497331 fatcat:cfcons6hrjeuhfna5z6b7fuiqi

Abstracts of the 2017 AANS/CNS Joint Section on Disorders of the Spine and Peripheral Nerves Las Vegas, Nevada • March 8–11, 2017

2017 Neurosurgical Focus  
Introduction: Cervical spondylotic myelopathy (CSM) is a common cause of spinal cord dysfunction.  ...  functional status in elderly patients undergoing elective spinal surgery for correction of adult degenerative scoliosis.  ...  suffering from spine and spinal cord injuries.  ... 
doi:10.3171/2017.3.foc-dspnabstracts pmid:28263664 fatcat:aoyncccuhjg5pd5ibk3iqdxvmq
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