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Marco Antonio Núñez-Gaona, Ricardo Marcelín-Jiménez, Josefina Gutiérrez-Martínez, Heriberto Aguirre-Meneses, José Luis Gonzalez-Compean
We present the construction of Babel, a distributed storage system that meets stringent requirements on dependability, availability, and scalability. Together with Babel, we developed an application that uses our system to store medical images. Accordingly, we show the feasibility of our proposal to provide an alternative solution for massive scientific storage and describe the software architecture style that manages the DICOM images life cycle, utilizing Babel like a virtual local storage component for a picture archiving and communication system (PACS-Babel Interface)...
May 18, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
Gokhan Bakal, Preetham Talari, Elijah V Kakani, Ramakanth Kavuluru
BACKGROUND: Identifying new potential treatment options for medical conditions that cause human disease burden is a central task of biomedical research. Since all candidate drugs cannot be tested with animal and clinical trials, in vitro approaches are first attempted to identify promising candidates. Likewise, identifying different causal relations between biomedical entities is also critical to understand biomedical processes. Generally, natural language processing (NLP) and machine learning are used to predict specific relations between any given pair of entities using the distant supervision approach...
May 12, 2018: Journal of Biomedical Informatics
Jose Antonio Miñarro-Giménez, Stefan Schulz
Organised repositories of published scientific literature represent a rich source for research in knowledge representation. MEDLINE, one of the largest and most popular biomedical literature databases, provides metadata for over 24 million articles each of which is indexed using the MeSH controlled vocabulary. In order to reuse MeSH annotations for knowledge construction, we processed this data and extracted the most relevant patterns of assigned descriptors over time. The patterns consist of UMLS semantic groups related to the MeSH headings together with their associated MeSH subheadings...
2018: Studies in Health Technology and Informatics
Raj Kumar Pandey, Salil Tewari, Lakshmi Tewari
A mycoremedial study was undertaken for decolourization of synthetic dyes using wood rot fungal culture Lenzites elegans WDP2. The culture was isolated from decaying wood as fruiting body, and identified on the basis of 5.8S ITS rRNA gene sequence analysis. Qualitative plate screening of culture showed extracellular laccase and lignin peroxidase production, while only laccase enzyme was produced in higher amount (156.793 Uml-1 ) in minimal salt broth medium containing glucose and veratryl alcohol. Laccase activity was increased up to 189...
April 12, 2018: Ecotoxicology and Environmental Safety
John Cuzzola, Ebrahim Bagheri, Jelena Jovanovic
Objective: The goal of this work is to map Unified Medical Language System (UMLS) concepts to DBpedia resources using widely accepted ontology relations from the Simple Knowledge Organization System (skos:exactMatch, skos:closeMatch) and from the Resource Description Framework Schema (rdfs:seeAlso), as a result of which a complete mapping from UMLS (UMLS 2016AA) to DBpedia (DBpedia 2015-10) is made publicly available that includes 221 690 skos:exactMatch, 26 276 skos:closeMatch, and 6 784 322 rdfs:seeAlso mappings...
April 10, 2018: Journal of the American Medical Informatics Association: JAMIA
Huanying Gu, Zhe He, Duo Wei, Gai Elhanan, Yan Chen
BACKGROUND: The UMLS assigns semantic types to all its integrated concepts. The semantic types are widely used in various natural language processing tasks in the biomedical domain, such as named entity recognition, semantic disambiguation, and semantic annotation. Due to the size of the UMLS, erroneous semantic type assignments are hard to detect. It is imperative to devise automated techniques to identify errors and inconsistencies in semantic type assignments. OBJECTIVES: Designing a methodology to perform programmatic checks to detect semantic type assignment errors for UMLS concepts with one or more SNOMED CT terms and evaluating concepts in a selected set of SNOMED CT hierarchies to verify our hypothesis that UMLS semantic type assignment errors may exist in concepts residing in semantically inconsistent groups...
February 2018: Methods of Information in Medicine
Andrew D Boyd, Karen Dunn Lopez, Camillo Lugaresi, Tamara Macieira, Vanessa Sousa, Sabita Acharya, Abhinaya Balasubramanian, Khawllah Roussi, Gail M Keenan, Yves A Lussier, Jianrong 'John' Li, Michel Burton, Barbara Di Eugenio
BACKGROUND: Physician and nurses have worked together for generations; however, their language and training are vastly different; comparing and contrasting their work and their joint impact on patient outcomes is difficult in light of this difference. At the same time, the EHR only includes the physician perspective via the physician-authored discharge summary, but not nurse documentation. Prior research in this area has focused on collaboration and the usage of similar terminology. OBJECTIVE: The objective of the study is to gain insight into interprofessional care by developing a computational metric to identify similarities, related concepts and differences in physician and nurse work...
May 2018: International Journal of Medical Informatics
Zachary M Grinspan, Niu Tian, Elissa G Yozawitz, Patricia E McGoldrick, Steven M Wolf, Tiffani L McDonough, Aaron Nelson, Baria Hafeez, Stephen B Johnson, Dale C Hesdorffer
Identifying individuals with rare epilepsy syndromes in electronic data sources is difficult, in part because of missing codes in the International Classification of Diseases (ICD) system. Our objectives were the following: (1) to describe the representation of rare epilepsies in other medical vocabularies, to identify gaps; and (2) to compile synonyms and associated terms for rare epilepsies, to facilitate text and natural language processing tools for cohort identification and population-based surveillance...
March 2018: Epilepsia Open
Andres Duque, Mark Stevenson, Juan Martinez-Romo, Lourdes Araujo
Word sense disambiguation is a key step for many natural language processing tasks (e.g. summarization, text classification, relation extraction) and presents a challenge to any system that aims to process documents from the biomedical domain. In this paper, we present a new graph-based unsupervised technique to address this problem. The knowledge base used in this work is a graph built with co-occurrence information from medical concepts found in scientific abstracts, and hence adapted to the specific domain...
March 21, 2018: Artificial Intelligence in Medicine
Zhiyong Yan, Feng Wang, Pingye Deng, Yu Wang, Kai Cai, Yanhui Chen, Zonghua Wang, Yang Liu
In this work, a novel and sensitive electrogenerated chemiluminescence (ECL) biosensor for protein kinase A (PKA) activity analysis and relevant inhibitor screening was proposed based on bimetallic catalysis signal amplification and recognition of Au and Pt nanoparticles loaded metal-organic frameworks (Au&Pt@UiO-66) nanocomposite. After being phosphorylated by PKA in the presence of ATP, Au&Pt@UiO-66 probes were specifically chelated to the modified electrode by forming Zr-O-P bonds between the surface defects of UiO-66 and the phosphorylated kemptide...
March 5, 2018: Biosensors & Bioelectronics
Nicolas Garcelon, Antoine Neuraz, Rémi Salomon, Hassan Faour, Vincent Benoit, Arthur Delapalme, Arnold Munnich, Anita Burgun, Bastien Rance
INTRODUCTION: Clinical data warehouses are often oriented toward integration and exploration of coded data. However narrative reports are of crucial importance for translational research. This paper describes Dr. Warehouse®, an open source data warehouse oriented toward clinical narrative reports and designed to support clinicians' day-to-day use. METHOD: Dr. Warehouse relies on an original database model to focus on documents in addition to facts. Besides classical querying functionalities, the system provides an advanced search engine and Graphical User Interfaces adapted to the exploration of text...
April 2018: Journal of Biomedical Informatics
Ricardo C Waldemarin, Cléver R G de Farias
A conceptual model abstractly defines a number of concepts and their relationships for the purposes of understanding and communication. Once a conceptual model is available, it can also be used as a starting point for the development of a software system. The development of conceptual models using the Unified Modeling Language (UML) facilitates the representation of modeled concepts and allows software developers to directly reuse these concepts in the design of a software system. The OBO Foundry represents the most relevant collaborative effort towards the development of ontologies in the biomedical domain...
April 2018: Journal of Biomedical Informatics
Bernd Neumayr, Christoph G Schuetz, Manfred A Jeusfeld, Michael Schrefl
An enterprise database contains a global, integrated, and consistent representation of a company's data. Multi-level modeling facilitates the definition and maintenance of such an integrated conceptual data model in a dynamic environment of changing data requirements of diverse applications. Multi-level models transcend the traditional separation of class and object with clabjects as the central modeling primitive, which allows for a more flexible and natural representation of many real-world use cases. In deep instantiation, the number of instantiation levels of a clabject or property is indicated by a single potency...
2018: Software and Systems Modeling
Alexander Bergmayr, Michael Grossniklaus, Manuel Wimmer, Gerti Kappel
The capability of UML profiles to serve as annotation mechanism has been recognized in both research and industry. Today's modeling tools offer profiles specific to platforms, such as Java, as they facilitate model-based engineering approaches. However, considering the large number of possible annotations in Java, manually developing the corresponding profiles would only be achievable by huge development and maintenance efforts. Thus, leveraging annotation-based modeling requires an automated approach capable of generating platform-specific profiles from Java libraries...
2018: Software and Systems Modeling
Raj Kumar Pandey, Khan Chand, Lakshmi Tewari
BACKGROUND: Lignocellulosic biomass from bamboo is an attractive feedstock for the bioethanol industry owing to its high cellulosic content and fast growth rate. In this study, powdery biomass was first enzymatically delignified and then saccharified using crude enzymes. RESULTS: The biological pretreatment decreased the lignin content of the biomass from an initial value of 295 to 137.7 g kg-1 , with a simultaneous increase in exposed cellulose content from 379...
February 13, 2018: Journal of the Science of Food and Agriculture
Noura El-Ahmady El-Naggar, Hoda M Soliman, Nancy M El-Shweihy
In recent years, microbial cholesterol oxidases have gained great attention due to its widespread use in medical applications for serum cholesterol determination. Streptomyces aegyptia strain NEAE-102 exhibited high level of extracellular cholesterol oxidase production using a minimum medium containing cholesterol as the sole source of carbon. Fifteen variables were screened using Plackett-Burman design for the enhanced cholesterol oxidase production. The most significant variables affecting enzyme production were further optimized by using the face-centered central composite design...
February 9, 2018: Scientific Reports
Dina Demner-Fushman, Sonya E Shooshan, Laritza Rodriguez, Alan R Aronson, Francois Lang, Willie Rogers, Kirk Roberts, Joseph Tonning
Adverse drug reactions (ADRs), unintended and sometimes dangerous effects that a drug may have, are one of the leading causes of morbidity and mortality during medical care. To date, there is no structured machine-readable authoritative source of known ADRs. The United States Food and Drug Administration (FDA) partnered with the National Library of Medicine to create a pilot dataset containing standardised information about known adverse reactions for 200 FDA-approved drugs. The Structured Product Labels (SPLs), the documents FDA uses to exchange information about drugs and other products, were manually annotated for adverse reactions at the mention level to facilitate development and evaluation of text mining tools for extraction of ADRs from all SPLs...
January 30, 2018: Scientific Data
Zhe He, Yehoshua Perl, Gai Elhanan, Yan Chen, James Geller, Jiang Bian
The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors do occur. Therefore, Quality Assurance efforts of UMLS curators for ST assignments should concentrate on automatically detected sets of UMLS concepts with higher error rates than random sets...
November 2017: Proceedings
Miguel Angel Canseco-Pérez, Genny Margarita Castillo-Avila, Bartolomé Chi-Manzanero, Ignacio Islas-Flores, Max M Apolinar-Hernández, Gerardo Rivera-Muñoz, Marcela Gamboa-Angulo, Felipe Sanchez-Teyer, Yeny Couoh-Uicab, Blondy Canto-Canché
A lipolytic screening with fungal strains isolated from lignocellulosic waste collected in banana plantation dumps was carried out. A Trichoderma harzianum strain (B13-1) showed good extracellular lipolytic activity (205 UmL-1 ). Subsequently, functional screening of the lipolytic activity on Rhodamine B enriched with olive oil as the only carbon source was performed. The successful growth of the strain allows us to suggest that a true lipase is responsible for the lipolytic activity in the B13-1 strain. In order to identify the gene(s) encoding the protein responsible for the lipolytic activity, in silico identification and characterization of triacylglycerol lipases from T...
January 25, 2018: Genes
John D Osborne, Matthew B Neu, Maria I Danila, Thamar Solorio, Steven J Bethard
BACKGROUND: Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated concepts") but the additional identifiers have been restricted to a defined set of relationships to the core concept. This approach limits the ability of the normalization process to express semantic meaning. We generated a freely available corpus using post-coordinated concepts without a defined set of relationships that we term "compositional concepts" to evaluate their use in clinical text...
January 10, 2018: Journal of Biomedical Semantics
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