Read by QxMD icon Read


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...
March 1, 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...
February 26, 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 appears as an attractive feedstock for bioethanol industry due to its high cellulosic content and fast growth rate. Therefore, powdery biomass was first enzymatically delignified and then saccharified using crude enzymes. RESULTS: The biological pretreatement decreased the lignin content of the biomass from an initial value of 29.5 to 8.4% with a simultaneous increase in exposed cellulose content from 37.93% to 61...
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
Tong Ruan, Mengjie Wang, Jian Sun, Ting Wang, Lu Zeng, Yichao Yin, Ju Gao
BACKGROUND: While a large number of well-known knowledge bases (KBs) in life science have been published as Linked Open Data, there are few KBs in Chinese. However, KBs in Chinese are necessary when we want to automatically process and analyze electronic medical records (EMRs) in Chinese. Of all, the symptom KB in Chinese is the most seriously in need, since symptoms are the starting point of clinical diagnosis. RESULTS: We publish a public KB of symptoms in Chinese, including symptoms, departments, diseases, medicines, and examinations as well as relations between symptoms and the above related entities...
September 20, 2017: Journal of Biomedical Semantics
Rui Antunes, Sérgio Matos
Word sense disambiguation (WSD) is an important step in biomedical text mining, which is responsible for assigning an unequivocal concept to an ambiguous term, improving the accuracy of biomedical information extraction systems. In this work we followed supervised and knowledge-based disambiguation approaches, with the best results obtained by supervised means. In the supervised method we used bag-of-words as local features, and word embeddings as global features. In the knowledge-based method we combined word embeddings, concept textual definitions extracted from the UMLS database, and concept association values calculated from the MeSH co-occurrence counts from MEDLINE articles...
December 13, 2017: Journal of Integrative Bioinformatics
Milad Moradi, Nasser Ghadiri
Automatic text summarization tools help users in the biomedical domain to acquire their intended information from various textual resources more efficiently. Some of biomedical text summarization systems put the basis of their sentence selection approach on the frequency of concepts extracted from the input text. However, it seems that exploring other measures rather than the raw frequency for identifying valuable contents within an input document, or considering correlations existing between concepts, may be more useful for this type of summarization...
January 2018: Artificial Intelligence in Medicine
Wei-Hung Weng, Kavishwar B Wagholikar, Alexa T McCray, Peter Szolovits, Henry C Chueh
BACKGROUND: The medical subdomain of a clinical note, such as cardiology or neurology, is useful content-derived metadata for developing machine learning downstream applications. To classify the medical subdomain of a note accurately, we have constructed a machine learning-based natural language processing (NLP) pipeline and developed medical subdomain classifiers based on the content of the note. METHODS: We constructed the pipeline using the clinical NLP system, clinical Text Analysis and Knowledge Extraction System (cTAKES), the Unified Medical Language System (UMLS) Metathesaurus, Semantic Network, and learning algorithms to extract features from two datasets - clinical notes from Integrating Data for Analysis, Anonymization, and Sharing (iDASH) data repository (n = 431) and Massachusetts General Hospital (MGH) (n = 91,237), and built medical subdomain classifiers with different combinations of data representation methods and supervised learning algorithms...
December 1, 2017: BMC Medical Informatics and Decision Making
Lihua Zhao, Hongliang Han, Zhanfang Ma
A new screen-printed carbon electrode (SPCE) with multiple working electrodes and one signal output channel without counter and reference electrodes was designed. The multiple working electrodes can be individually modified for each target of interest. The SPCE contained one signal output channel, making the immuniosensor be realized by common single-channel electrochemical workstation. The counter and reference electrodes were independent of disposable SPCE, reducing costs and eliminating precious metal pollution...
October 19, 2017: Biosensors & Bioelectronics
Jinmeng Jia, Zhongxin An, Yue Ming, Yongli Guo, Wei Li, Yunxiang Liang, Dongming Guo, Xin Li, Jun Tai, Geng Chen, Yaqiong Jin, Zhimei Liu, Xin Ni, Tieliu Shi
Rare diseases affect over a hundred million people worldwide, most of these patients are not accurately diagnosed and effectively treated. The limited knowledge of rare diseases forms the biggest obstacle for improving their treatment. Detailed clinical phenotyping is considered as a keystone of deciphering genes and realizing the precision medicine for rare diseases. Here, we preset a standardized system for various types of rare diseases, called encyclopedia of Rare disease Annotations for Precision Medicine (eRAM)...
November 2, 2017: Nucleic Acids Research
Jun Gao, Ninghao Liu, Mark Lawley, Xia Hu
Online healthcare forums (OHFs) have become increasingly popular for patients to share their health-related experiences. The healthcare-related texts posted in OHFs could help doctors and patients better understand specific diseases and the situations of other patients. To extract the meaning of a post, a commonly used way is to classify the sentences into several predefined categories of different semantics. However, the unstructured form of online posts brings challenges to existing classification algorithms...
2017: Journal of Healthcare Engineering
Jung-Wei Fan, Jianrong Li, Yves A Lussier
Exposome is a critical dimension in the precision medicine paradigm. Effective representation of exposomics knowledge is instrumental to melding nongenetic factors into data analytics for clinical research. There is still limited work in (1) modeling exposome entities and relations with proper integration to mainstream ontologies and (2) systematically studying their presence in clinical context. Through selected ontological relations, we developed a template-driven approach to identifying exposome concepts from the Unified Medical Language System (UMLS)...
2017: Journal of Healthcare Engineering
Jun Gao, Ninghao Liu, Mark Lawley, Xia Hu
Online healthcare forums (OHFs) have become increasingly popular for patients to share their health-related experiences. The healthcare-related texts posted in OHFs could help doctors and patients better understand specific diseases and the situations of other patients. To extract the meaning of a post, a commonly used way is to classify the sentences into several predefined categories of different semantics. However, the unstructured form of online posts brings challenges to existing classification algorithms...
2017: Journal of Healthcare Engineering
Yuqun Zeng, Xusheng Liu, Yanshan Wang, Feichen Shen, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, Hongfang Liu
BACKGROUND: Self-management is crucial to diabetes care and providing expert-vetted content for answering patients' questions is crucial in facilitating patient self-management. OBJECTIVE: The aim is to investigate the use of information retrieval techniques in recommending patient education materials for diabetic questions of patients. METHODS: We compared two retrieval algorithms, one based on Latent Dirichlet Allocation topic modeling (topic modeling-based model) and one based on semantic group (semantic group-based model), with the baseline retrieval models, vector space model (VSM), in recommending diabetic patient education materials to diabetic questions posted on the TuDiabetes forum...
October 16, 2017: Journal of Medical Internet Research
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"