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https://www.readbyqxmd.com/read/30087946/challenges-of-connecting-chemistry-to-pharmacology-perspectives-from-curating-the-iuphar-bps-guide-to-pharmacology
#1
REVIEW
Christopher Southan, Joanna L Sharman, Elena Faccenda, Adam J Pawson, Simon D Harding, Jamie A Davies
Connecting chemistry to pharmacology has been an objective of Guide to PHARMACOLOGY (GtoPdb) and its precursor the International Union of Basic and Clinical Pharmacology Database (IUPHAR-DB) since 2003. This has been achieved by populating our database with expert-curated relationships between documents, assays, quantitative results, chemical structures, their locations within the documents, and the protein targets in the assays (D-A-R-C-P). A wide range of challenges associated with this are described in this perspective, using illustrative examples from GtoPdb entries...
July 31, 2018: ACS Omega
https://www.readbyqxmd.com/read/30074992/web-monitoring-of-emerging-animal-infectious-diseases-integrated-in-the-french-animal-health-epidemic-intelligence-system
#2
Elena Arsevska, Sarah Valentin, Julien Rabatel, Jocelyn de Goër de Hervé, Sylvain Falala, Renaud Lancelot, Mathieu Roche
Since 2013, the French Animal Health Epidemic Intelligence System (in French: Veille Sanitaire Internationale, VSI) has been monitoring signals of the emergence of new and exotic animal infectious diseases worldwide. Once detected, the VSI team verifies the signals and issues early warning reports to French animal health authorities when potential threats to France are detected. To improve detection of signals from online news sources, we designed the Platform for Automated extraction of Disease Information from the web (PADI-web)...
2018: PloS One
https://www.readbyqxmd.com/read/30065857/an-automated-identification-and-analysis-of-ontological-terms-in-gastrointestinal-diseases-and-nutrition-related-literature-provides-useful-insights
#3
Orges Koci, Michael Logan, Vaios Svolos, Richard K Russell, Konstantinos Gerasimidis, Umer Zeeshan Ijaz
With an unprecedented growth in the biomedical literature, keeping up to date with the new developments presents an immense challenge. Publications are often studied in isolation of the established literature, with interpretation being subjective and often introducing human bias. With ontology-driven annotation of biomedical data gaining popularity in recent years and online databases offering metatags with rich textual information, it is now possible to automatically text-mine ontological terms and complement the laborious task of manual management, interpretation, and analysis of the accumulated literature with downstream statistical analysis...
2018: PeerJ
https://www.readbyqxmd.com/read/30055354/the-contribution-of-mitochondrial-metagenomics-to-large-scale-data-mining-and-phylogenetic-analysis-of-coleoptera
#4
Benjamin Linard, Alex Crampton-Platt, Jérome Moriniere, Martijn J T N Timmermans, Carmelo Andujar, Paula Arribas, Kirsten E Miller, Julia Lipecki, Emeline Favreau, Amie Hunter, Carola Gómez-Rodríguez, Christopher Barton, Ruie Nie, Conrad P D T Gillett, Thijmen Breeschoten, Ladislav Bocak, Alfried P Vogler
A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp...
July 25, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/30044790/mapping-the-yearly-extent-of-surface-coal-mining-in-central-appalachia-using-landsat-and-google-earth-engine
#5
Andrew A Pericak, Christian J Thomas, David A Kroodsma, Matthew F Wasson, Matthew R V Ross, Nicholas E Clinton, David J Campagna, Yolandita Franklin, Emily S Bernhardt, John F Amos
Surface mining for coal has taken place in the Central Appalachian region of the United States for well over a century, with a notable increase since the 1970s. Researchers have quantified the ecosystem and health impacts stemming from mining, relying in part on a geospatial dataset defining surface mining's extent at a decadal interval. This dataset, however, does not deliver the temporal resolution necessary to support research that could establish causal links between mining activity and environmental or public health and safety outcomes, nor has it been updated since 2005...
2018: PloS One
https://www.readbyqxmd.com/read/30039404/enalos-knime-nodes-new-cheminformatics-tools-for-drug-discovery
#6
Dimitra-Danai Varsou, Spyridon Nikolakopoulos, Andreas Tsoumanis, Georgia Melagraki, Antreas Afantitis
In this chapter we present and discuss Enalos+ nodes designed and developed by NovaMechanics Ltd. for the open-source KNIME platform, as a useful aid when dealing with cheminformatics and nanoinformatics problems or medicinal applications. Enalos+ nodes facilitate tasks performed in molecular modeling and allow access, data mining, and manipulation for multiple chemical databases through the KNIME interface. Enalos+ nodes automate common procedures that greatly facilitate the rapid workflow prototyping within KNIME...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30035154/deeplesion-automated-mining-of-large-scale-lesion-annotations-and-universal-lesion-detection-with-deep-learning
#7
Ke Yan, Xiaosong Wang, Le Lu, Ronald M Summers
Extracting, harvesting, and building large-scale annotated radiological image datasets is a greatly important yet challenging problem. Meanwhile, vast amounts of clinical annotations have been collected and stored in hospitals' picture archiving and communication systems (PACS). These types of annotations, also known as bookmarks in PACS, are usually marked by radiologists during their daily workflow to highlight significant image findings that may serve as reference for later studies. We propose to mine and harvest these abundant retrospective medical data to build a large-scale lesion image dataset...
July 2018: Journal of Medical Imaging
https://www.readbyqxmd.com/read/30018200/a-smart-sensing-architecture-for-domestic-monitoring-methodological-approach-and-experimental-validation
#8
Andrea Monteriù, Mario Rosario Prist, Emanuele Frontoni, Sauro Longhi, Filippo Pietroni, Sara Casaccia, Lorenzo Scalise, Annalisa Cenci, Luca Romeo, Riccardo Berta, Loreto Pescosolido, Gianni Orlandi, Gian Marco Revel
Smart homes play a strategic role for improving life quality of people, enabling to monitor people at home with numerous intelligent devices. Sensors can be installed to provide a continuous assistance without limiting the resident's daily routine, giving her/him greater comfort, well-being and safety. This paper is based on the development of domestic technological solutions to improve the life quality of citizens and monitor the users and the domestic environment, based on features extracted from the collected data...
July 17, 2018: Sensors
https://www.readbyqxmd.com/read/30014161/occupational-emphysema-in-south-african-miners-at-autopsy-1975-2014
#9
Sithembile L Mabila, Kirsten S Almberg, Lee Friedman, Robert Cohen, Ntombizodwa Ndlovu, Naseema Vorajee, Jill Murray
PURPOSE: To determine the associations between exposure duration, measured by employment tenure, and emphysema presence and severity in black and white South African miners at autopsy. METHODS: We examined the association between mining tenure and emphysema presence or severity using the Pathology Automation (PATHAUT) database, 1975-2014. We used logistic regression models adjusted for age, tuberculosis, HIV status, and year of death. The effect of smoking on the presence and severity of emphysema was assessed in a sub-analysis of white miners...
July 16, 2018: International Archives of Occupational and Environmental Health
https://www.readbyqxmd.com/read/30013060/the-evolving-interface-between-synthetic-biology-and-functional-metagenomics
#10
REVIEW
Eric van der Helm, Hans J Genee, Morten O A Sommer
Nature is a diverse and rich source of bioactive pathways or novel building blocks for synthetic biology. In this Perspective, we describe the emerging research field in which metagenomes are functionally interrogated using synthetic biology. This approach substantially expands the set of identified biological activities and building blocks. In reviewing this field, we find that its potential for new biological discovery is dramatically increasing. Functional metagenomic mining using genetic circuits has led to the discovery of novel bioactivity such as amidases, NF-κB modulators, naphthalene degrading enzymes, cellulases, lipases and transporters...
August 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29992320/identifying-frequent-patterns-in-biochemical-reaction-networks-a-workflow
#11
Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel
Computational models in biology encode molecular and cell biological processes. Many of these models can be represented as biochemical reaction networks. Studying such networks, one is mostly interested in systems that share similar reactions and mechanisms. Typical goals of an investigation thus include understanding of model parts, identification of reoccurring patterns and recognition of biologically relevant motifs. The large number and size of available models, however, require automated methods to support researchers in achieving their goals...
January 1, 2018: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29990115/classification-of-medical-images-in-the-biomedical-literature-by-jointly-using-deep-and-handcrafted-visual-features
#12
Jianpeng Zhang, Yong Xia, Yutong Xie, Michael Fulham, Dagan Feng
The classification of medical images and illustrations from the biomedical literature is important for automated literature review, retrieval and mining. Although deep learning is effective for large-scale image classification, it may not be the optimal choice for this task as there is only a small training dataset. We propose a combined deep and handcrafted visual feature (CDHVF) based algorithm that uses features learned by three fine-tuned and pre-trained deep convolutional neural networks (DCNNs) and two handcrafted descriptors in a joint approach...
November 20, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/29981872/extending-pubmed-searches-to-clinicaltrials-gov-through-a-machine-learning-approach-for-systematic-reviews
#13
Corrado Lanera, Clara Minto, Abhinav Sharma, Dario Gregori, Paola Berchialla, Ileana Baldi
AIMS: Despite their essential role in collecting and organizing published medical literature, indexed search engines are unable to cover all relevant knowledge. Hence, current literature recommends the inclusion of clinical trial registries in systematic reviews. This study aims to provide an automated approach to extend a search on PubMed to the ClinicalTrials.gov database, relying on text mining and machine learning techniques. STUDY DESIGN AND SETTING: The procedure starts from a literature search on PubMed...
July 5, 2018: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/29956454/automated-data-mining-of-a-plan-check-database-and-example-application
#14
Leon Dunn, David Jolly
PURPOSE: The aim of this work was to present the development and example application of an automated data mining software platform that preforms bulk analysis of results and patient data passing through the 3D plan and delivery QA system, Mobius3D. METHODS: Python, matlab, and Java were used to create an interface that reads JavaScript Object Notation (JSON) created for every approved Mobius3D pre-treatment plan-check. The aforementioned JSON files contain all the information for every pre-treatment QA check performed by Mobius3D, including all 3D dose, CT, structure set information, as well as all plan information and patient demographics...
June 29, 2018: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/29954318/famplex-a-resource-for-entity-recognition-and-relationship-resolution-of-human-protein-families-and-complexes-in-biomedical-text-mining
#15
John A Bachman, Benjamin M Gyori, Peter K Sorger
BACKGROUND: For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers, a process known as named entity linking or "grounding." Correct grounding is essential for resolving relationships among mined information, curated interaction databases, and biological datasets. The accuracy of this process is largely dependent on the availability of machine-readable resources associating synonyms and abbreviations commonly found in biomedical literature with uniform identifiers...
June 28, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29934377/four-decades-of-pulmonary-tuberculosis-in-deceased-south-african-miners-trends-and-determinants
#16
Ntombizodwa Ndlovu, Eustasius Musenge, Sung Kyun Park, Brendan Girdler-Brown, Guy Richards, Jill Murray
OBJECTIVE: We investigated trends and determinants of pulmonary tuberculosis (PTB) in deceased South African miners. METHODS: Statutory autopsies are performed on miners for occupational lung disease compensation, irrespective of cause of death. Data were extracted from the PATHAUT (Pathology Automation System) autopsy database. PTB trends were analysed and explanatory variables (year of autopsy, age at death, gold employment duration, silicosis and HIV) were evaluated using binary logistic regression modelling...
June 22, 2018: Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/29929223/biochar-affects-the-dissolved-and-colloidal-concentrations-of-cd-cu-ni-and-zn-and-their-phytoavailability-and-potential-mobility-in-a-mining-soil-under-dynamic-redox-conditions
#17
Ali El-Naggar, Sabry M Shaheen, Yong Sik Ok, Jörg Rinklebe
There is a lack of knowledge on the effects of biochar (BC) on the release dynamics of potentially toxic elements (PTEs) in different phases of soil under systematic change of redox potential (EH ). We aimed to elucidate the impact of pre-definite EH on the release dynamics of dissolved and colloidal concentrations of Cd, Cu, Ni, and Zn as well as their phytoavailability and potential mobility in the solid-phase of a mining soil treated with rice hull biochar (S+BC) compared to non-treated soil (S). The influence of EH -dependent changes of soil pH, dissolved organic carbon (DOC), dissolved aromatic carbon (DAC), Fe, Mn, SO4 2- , and Cl- on the elements release was also determined...
May 15, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29904019/automated-recognition-of-rna-structure-motifs-by-their-shape-data-signatures
#18
Pierce Radecki, Mirko Ledda, Sharon Aviran
High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest are RNA elements whose underlying structures are necessary for their biological functions. We previously introduced patteRNA , an algorithm for rapidly mining SP data for patterns characteristic of such motifs. This work provided a proof-of-concept for the detection of motifs and the capability of distinguishing structures displaying pronounced conformational changes...
June 14, 2018: Genes
https://www.readbyqxmd.com/read/29898743/utility-of-social-media-and-crowd-intelligence-data-for-pharmacovigilance-a-scoping-review
#19
Andrea C Tricco, Wasifa Zarin, Erin Lillie, Serena Jeblee, Rachel Warren, Paul A Khan, Reid Robson, Ba' Pham, Graeme Hirst, Sharon E Straus
BACKGROUND: A scoping review to characterize the literature on the use of conversations in social media as a potential source of data for detecting adverse events (AEs) related to health products. METHODS: Our specific research questions were (1) What social media listening platforms exist to detect adverse events related to health products, and what are their capabilities and characteristics? (2) What is the validity and reliability of data from social media for detecting these adverse events? MEDLINE, EMBASE, Cochrane Library, and relevant websites were searched from inception to May 2016...
June 14, 2018: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/29880698/evidence-synthesis-software
#20
Sophie Elizabeth Park, James Thomas
It can be challenging to decide which evidence synthesis software to choose when doing a systematic review. This article discusses some of the important questions to consider in relation to the chosen method and synthesis approach. Software can support researchers in a range of ways. Here, a range of review conditions and software solutions. For example, facilitating contemporaneous collaboration across time and geographical space; in-built bias assessment tools; and line-by-line coding for qualitative textual analysis...
June 7, 2018: BMJ evidence-based medicine
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