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An Evolutionary Approach to the Annotation of Discharge Summaries

Christina Lohr, Luise Modersohn, Johannes Hellrich, Tobias Kolditz, Udo Hahn
2020 Studies in Health Technology and Informatics  
We here describe the evolution of annotation guidelines for major clinical named entities, namely Diagnosis, Findings and Symptoms, on a corpus of approximately 1,000 German discharge letters.  ...  Due to their intrinsic opaqueness and complexity, clinical annotation tasks require continuous guideline tuning, beginning from the initial definition of crucial entities and the subsequent iterative evolution  ...  We thank all annotators, as well as Andre ´ Scherag, Danny Ammon, and all members of the Data Integration Center of the Jena University Hospital.  ... 
doi:10.3233/shti200116 pmid:32570340 fatcat:5pbaysmnszc7fnhn437y5gvzsq

Laying the groundwork for enterprise-wide medical language processing services: architecture and process

Elizabeth S Chen, Francine L Maloney, Eugene Shilmayster, Howard S Goldberg
2009 AMIA Annual Symposium Proceedings  
Key objectives included exploring the use of an open-source framework called the Unstructured Information Management Architecture (UIMA) and leveraging existing MLP-related efforts, terminology, and document  ...  This paper describes early experiences in defining the infrastructure and standards for extracting, encoding, and structuring clinical observations from a variety of clinical documents to serve enterprise-wide  ...  The authors are thankful to many for their contributions to the project: Cheryl Van Putten, Eugene Breydo, Alexander Kheyfets, Alexander Turchin, Adam Wright, Michael Vashevko, and Jonathan Einbinder.  ... 
pmid:20351830 pmcid:PMC2815370 fatcat:saahwrdwhzgxnmald4unigoywi

Firing the Sting: Chemically Induced Discharge of Cnidae Reveals Novel Proteins and Peptides from Box Jellyfish (Chironex fleckeri) Venom

Mahdokht Jouiaei, Nicholas Casewell, Angel Yanagihara, Amanda Nouwens, Bronwen Cribb, Darryl Whitehead, Timothy Jackson, Syed Ali, Simon Wagstaff, Ivan Koludarov, Paul Alewood, Jay Hansen (+1 others)
2015 Toxins  
Further, to investigate nematocyst content or "venom" recovery, we utilized both top-down and bottom-up transcriptomics-proteomics approaches and compared the proteome profile of this new ethanol recovery  ...  Cnidarian venom research has lagged behind other toxinological fields due to technical difficulties in recovery of the complex venom from the microscopic nematocysts.  ...  Moreover, due to the lack of a transcriptomic database underpinning the annotation of the isolated proteins, proteomic approaches were unlikely to discover novel toxins unique to this species.  ... 
doi:10.3390/toxins7030936 pmid:25793725 pmcid:PMC4379534 fatcat:j2yxmwlvtjf3vne5up62dvixdi

Comparing reference-based RNA-Seq mapping methods for non-human primate data

Ashlee M Benjamin, Marshall Nichols, Thomas W Burke, Geoffrey S Ginsburg, Joseph E Lucas
2014 BMC Genomics  
We utilize TopHat2 and GSNAP for mapping to the human genome, and Bowtie2 and Stampy for mapping to the human genome and transcriptome for a total of six mapping approaches.  ...  Critical algorithm features include short seed sequences, the allowance of mismatches, and the allowance of gapped alignments in addition to splice junction gaps.  ...  Acknowledgements We would like to acknowledge the support of the NIH CTSA (Clinical and Translational Science Award) 1UL1RR024128-01, and the Gates Foundation, number OPP1017554 (G.S.G.).  ... 
doi:10.1186/1471-2164-15-570 pmid:25001289 pmcid:PMC4112205 fatcat:cu6e3zz7g5c4taih4bgkyocewe

Biogeochemistry of Major World Rivers, Scope 42 edited by E.T. Degens, S. Kempe, and J.E. Richey, John Wiley, Chichester, 1991. 356 pp. Price: £85.00

K. R. Dyer
1991 Aquatic conservation  
The structure and contents of these chapters vary; in most there is an appraisal of the possible evolutionary histories of the respective floras.  ...  A final summary chapter brings together the results from the rest of the book and provides useful extensive tables of river drainage areas, water discharges, and dissolved and suspended solids, and organic  ... 
doi:10.1002/aqc.3270010209 fatcat:5zuk56hpffhhthbrqdv5hmanam

Medical Knowledge Embedding Based on Recursive Neural Network for Multi-Disease Diagnosis [article]

Jingchi Jiang, Huanzheng Wang, Jing Xie, Xitong Guo, Yi Guan, Qiubin Yu
2018 arXiv   pre-print
., high-dimensional and continuous vectors) is a feasible approach to complex reasoning that can not only retain the semantic information of knowledge but also establish the quantifiable relationship among  ...  Experimental results verify that the diagnostic accuracy of RNKN is superior to that of some classical machine learning models and Markov logic network (MLN).  ...  ACKNOWLEDGMENT The Chinese Electronic Medical Records used in this paper were provided by Second Affiliated Hospital of Harbin Medical University.  ... 
arXiv:1809.08422v1 fatcat:tgaazzlpkvcwvi2jaxhl4kqd54

Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting

Chun-Ji Li, Die Zhao, Bing-Xue Li, Ning Zhang, Jian-Yu Yan, Hong-Tao Zou
2020 BMC Genomics  
A phylogenetic assessment suggested that the evolutionary trajectory of the order Sporidiobolales species was evolved from genus Sporobolomyces to Rhodotorula through the mediator Rhodosporidiobolus.  ...  Through the annotation information of the genome, we screened many key genes involved in carotenoids, lipids, carbohydrate metabolism and signal transduction pathways.  ...  Acknowledgements The authors would like to express gratitude to all those who helped us during the writing of this paper.  ... 
doi:10.1186/s12864-020-6593-1 pmid:32093624 fatcat:xjmk75hpsrhlrj4itt5h3mplcy

Concurrent Development of Model and Implementation [article]

A.Gravell and Y. Howard and J.C. Augusto and C. Ferreira and S. Gruner
2011 arXiv   pre-print
Recommendations are therefore made for future improvements to tools supporting formal models which would, in principle, make this co-evolutionary approach attractive to industrial software developers.  ...  A number of techniques are listed can make use of such a model to enhance the development process, and also ways to keep model and implementation consistent.  ...  The classical approach is to verify the specification against the model using formal proof. This is rather heavyweight, and not appropriate in the context of an evolutionary or agile method.  ... 
arXiv:1111.2826v1 fatcat:svy5mu2fmze2dddyndsizommo4

Computational Methods for the Analysis of Primate Mobile Elements [chapter]

Richard Cordaux, Shurjo K. Sen, Miriam K. Konkel, Mark A. Batzer
2010 Msphere  
Insights into these questions have come in part from the development of computational methods that allow detailed and reliable identification, annotation, and evolutionary analyses of the many TE families  ...  Transposable elements (TE), defined as discrete pieces of DNA that can move from one site to another site in genomes, represent significant components of eukaryotic genomes, including primates.  ...  Acknowledgments Our research is supported by National Science Foundation BCS-0218338 (MAB) and EPS-0346411 (MAB), National Institutes of Health RO1 GM59290 (MAB) and PO1 AG022064 (MAB), and the State of  ... 
doi:10.1007/978-1-60327-367-1_8 pmid:20238080 pmcid:PMC2880165 fatcat:zwb76jmsargcvcsuax4kxd5jda

Enzymes of early-diverging, zoosporic fungi

Lene Lange, Kristian Barrett, Bo Pilgaard, Frank Gleason, Adrian Tsang
2019 Applied Microbiology and Biotechnology  
The secretome, the complement of extracellular proteins, is a reflection of the interaction of an organism with its host or substrate, thus a determining factor for the organism's fitness and competitiveness  ...  The approach taken by the review enables comparison of the secretome enzyme composition of anaerobic versus aerobic early-diverging fungi and comparison of enzyme portfolio of specialized parasites, pathogens  ...  Acknowledgments Review on "Enzymes of early-diverging, zoosporic  ... 
doi:10.1007/s00253-019-09983-w pmid:31309267 pmcid:PMC6690862 fatcat:qoilegemkjeanexp6bgyt2lxfa

Development of a Novel Multimedia E-Learning Tool for Teaching the Symptoms and Signs of Stroke

Jonathan Birns, Peter Woodward, Harry Brenton, Fernando Bello
2018 Creative Education  
An iterative, evolutionary, action research approach was employed to build the e-learning tool around an array of acute neurological scenarios of stroke and stroke-mimic presentations.  ...  A number of approaches were explored for visually demonstrating the effects of functional impairment in stroke patients using animations and juxtaposing brain imaging scans and 3D models.  ...  Conflict of Interest Statement There are no conflicts of interest.  ... 
doi:10.4236/ce.2018.98089 fatcat:jmjc335ddndidjpffwkaae3r6y

Genome-resolved insight into the reservoir of antibiotic resistance genes in an aquatic microbial community [article]

Zahra Goodarzi, Sedigheh Asad, Maliheh Mehrshad
2022 bioRxiv   pre-print
Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile.  ...  We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes  ...  Acknowledgements: The computational analysis was performed at the Center for High-Performance Computing, School of Mathematics, Statistics, and Computer Science, University of Tehran.  ... 
doi:10.1101/2022.08.30.505784 fatcat:5ziaxoa2rnc7tfqxfravo6h3iq

The evolutionary history of manatees told by their mitogenomes

Érica Martinha Silva de Souza, Lucas Freitas, Elisa Karen da Silva Ramos, Giovanna Selleghin-Veiga, Michelle Carneiro Rachid-Ribeiro, Felipe André Silva, Miriam Marmontel, Fabrício Rodrigues dos Santos, Anne Laudisoit, Erik Verheyen, Daryl P. Domning, Mariana Freitas Nery
2021 Scientific Reports  
We use full mitogenomes of all extant manatee species to infer the divergence dates and biogeographical histories of these species and the effect of natural selection on their mitogenomes.  ...  In conclusion, our results provide novel insight into the evolutionary history of the Trichechidae during the Late Miocene, which was influenced by geological events, such as Amazon Basin formation.  ...  AL and EV thank the ICCN for providing CITES certificate 6543 export of the T. senegalensis sample we used, originating from the Park Marin de Mangroves of the DR Congo.  ... 
doi:10.1038/s41598-021-82390-2 pmid:33574363 pmcid:PMC7878490 fatcat:z2k3uehbkjdgfk5cx67ywt7z4y

Genetic basis for the establishment of endosymbiosis in Paramecium

Ming He, Jinfeng Wang, Xinpeng Fan, Xiaohui Liu, Wenyu Shi, Ning Huang, Fangqing Zhao, Miao Miao
2019 The ISME Journal  
To elucidate the mechanism of this type of endosymbiosis, we combined PacBio and Illumina sequencing to assemble a high-quality and near-complete macronuclear genome of P. bursaria.  ...  The single-celled ciliate Paramecium bursaria is an indispensable model for investigating endosymbiosis between protists and green-algal symbionts.  ...  Acknowledgements This work was supported by grants from the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (2018SDKJ0406-2) and National Natural Science  ... 
doi:10.1038/s41396-018-0341-4 pmid:30647459 pmcid:PMC6474222 fatcat:lbyeaslsbbaxtpednqnhxwkgzi

The case for sequencing the genome of the electric eel Electrophorus electricus

J. S. Albert, H. H. Zakon, P. K. Stoddard, G. A. Unguez, S. K. S. Holmberg-Albert, M. R. Sussman
2008 Journal of Fish Biology  
Over tens of millions of years, electric fish have evolved an exceptional capacity to generate a weak (millivolt) electric field in the water near their body from specialized muscle-derived electric organs  ...  Understanding the regulation of ion channel genes will be central for efforts to induce the differentiation of electrogenic cells in other tissues and organisms and to control the intrinsic electric behaviours  ...  The discharge of the electric organ creates an electric field in the water around the fish.  ... 
doi:10.1111/j.1095-8649.2007.01631.x fatcat:7y6isfjb2vfkhklbzqou2fgxvi
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