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https://www.readbyqxmd.com/read/28339805/design-and-evaluation-of-a-pharmacogenomics-information-resource-for-pharmacists
#1
Katrina M Romagnoli, Richard D Boyce, Philip E Empey, Yifan Ning, Solomon Adams, Harry Hochheiser
Objective: To develop and evaluate a pharmacogenomics information resource for pharmacists. Materials and Methods: We built a pharmacogenomics information resource presenting Food and Drug Administration (FDA) drug product labelling information, refined it based on feedback from pharmacists, and conducted a comparative usability evaluation, measuring task completion time, task correctness and perceived usability. Tasks involved hypothetical clinical situations requiring interpretation of pharmacogenomics information to determine optimal prescribing for specific patients...
February 26, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339629/orders-on-file-but-no-labs-drawn-investigation-of-machine-and-human-errors-caused-by-an-interface-idiosyncrasy
#2
Richard Schreiber, Dean F Sittig, Joan Ash, Adam Wright
In this report, we describe 2 instances in which expert use of an electronic health record (EHR) system interfaced to an external clinical laboratory information system led to unintended consequences wherein 2 patients failed to have laboratory tests drawn in a timely manner. In both events, user actions combined with the lack of an acknowledgment message describing the order cancellation from the external clinical system were the root causes. In 1 case, rapid, near-simultaneous order entry was the culprit; in the second, astute order management by a clinician, unaware of the lack of proper 2-way interface messaging from the external clinical system, led to the confusion...
February 16, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28335431/building-a-relationship-between-robot-characteristics-and-teleoperation-user-interfaces
#3
Michael Mortimer, Ben Horan, Mehdi Seyedmahmoudian
The Robot Operating System (ROS) provides roboticists with a standardized and distributed framework for real-time communication between robotic systems using a microkernel environment. This paper looks at how ROS metadata, Unified Robot Description Format (URDF), Semantic Robot Description Format (SRDF), and its message description language, can be used to identify key robot characteristics to inform User Interface (UI) design for the teleoperation of heterogeneous robot teams. Logical relationships between UI components and robot characteristics are defined by a set of relationship rules created using relevant and available information including developer expertise and ROS metadata...
March 14, 2017: Sensors
https://www.readbyqxmd.com/read/28334930/rcas-an-rna-centric-annotation-system-for-transcriptome-wide-regions-of-interest
#4
Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334349/deepbluer-large-scale-epigenomic-analysis-in-r
#5
Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer
Motivation: While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. The DeepBlue Epigenomic Data Server provides a powerful interface and API for filtering, transforming, aggregating and downloading data from several epigenomic consortia. Results: To make public epigenomic data conveniently available for analysis in R, we developed an R/Bioconductor package that connects to the DeepBlue Epigenomic Data Server, enabling users to quickly gather and transform epigenomic data from selected experiments for analysis in the Bioconductor ecosystem...
February 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334120/svpv-a-structural-variant-prediction-viewer-for-paired-end-sequencing-datasets
#6
Jacob E Munro, Sally L Dunwoodie, Eleni Giannoulatou
Motivation: A wide range of algorithms exist for the prediction of structural variants (SVs) from paired-end whole genome sequencing (WGS) alignments. It is essential for the purpose of quality control to be able to visualize, compare and contrast the data underlying the predictions across multiple different algorithms. Results: We provide the structural variant prediction viewer, a tool which presents a visual summary of the most relevant features for SV prediction from WGS data...
February 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333085/ebasis-bioactive-substances-in-food-information-systems-and-bioactive-intakes-major-updates-of-the-bioactive-compound-composition-and-beneficial-bioeffects-database-and-the-development-of-a-probabilistic-model-to-assess-intakes-in-europe
#7
Jenny Plumb, Sandrine Pigat, Foteini Bompola, Maeve Cushen, Hannah Pinchen, Eric Nørby, Siân Astley, Jacqueline Lyons, Mairead Kiely, Paul Finglas
eBASIS (Bioactive Substances in Food Information Systems), a web-based database that contains compositional and biological effects data for bioactive compounds of plant origin, has been updated with new data on fruits and vegetables, wheat and, due to some evidence of potential beneficial effects, extended to include meat bioactives. eBASIS remains one of only a handful of comprehensive and searchable databases, with up-to-date coherent and validated scientific information on the composition of food bioactives and their putative health benefits...
March 23, 2017: Nutrients
https://www.readbyqxmd.com/read/28331566/person-centered-prediction-of-survival-in-population-based-screening-program-by-an-intelligent-clinical-decision-support-system
#8
Reza Safdari, Elham Maserat, Hamid Asadzadeh Aghdaei, Amir Hossein Javan Amoli, Hamid Mohaghegh Shalmani
AIM: To survey person centered survival rate in population based screening program by an intelligent clinical decision support system. BACKGROUND: Colorectal cancer is the most common malignancy and major cause of morbidity and mortality throughout the world. Colorectal cancer is the sixth leading cause of cancer death in Iran. In this survey, we used cosine similarity as data mining technique and intelligent system for estimating survival of at risk groups in the screening plan...
2017: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28330138/vdap-gui-a-user-friendly-pipeline-for-variant-discovery-and-annotation-of-raw-next-generation-sequencing-data
#9
Ramesh Menon, Namrata V Patel, Amitbikram Mohapatra, Chaitanya G Joshi
Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328499/importance-of-matching-physical-friction-hardness-and-texture-in-creating-realistic-haptic-virtual-surfaces
#10
Heather Culbertson, Katherine J Kuchenbecker
Interacting with physical objects through a tool elicits tactile and kinesthetic sensations that comprise your haptic impression of the object. These cues, however, are largely missing from interactions with virtual objects, yielding an unrealistic user experience. This article evaluates the realism of virtual surfaces rendered using haptic models constructed from data recorded during interactions with real surfaces. The models include three components: surface friction, tapping transients, and texture vibrations...
January 2017: IEEE Transactions on Haptics
https://www.readbyqxmd.com/read/28327936/guidock-vnc-using-a-graphical-desktop-sharing-system-to-provide-a-browser-based-interface-for-containerized-software
#11
Varun Mittal, Ling-Hong Hung, Jayant Keswani, Daniel Kristiyanto, Sung Bong Lee, Ka Yee Yeung
Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line based tool and many bioinformatics pipelines consist of components that require a graphical user interface. Findings: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327601/bcip-a-gene-centered-platform-for-identifying-potential-regulatory-genes-in-breast-cancer
#12
Jiaqi Wu, Shuofeng Hu, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, Xiaomin Ying
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327092/metax-a-flexible-and-comprehensive-software-for-processing-metabolomics-data
#13
Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
BACKGROUND: Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated from mass spectrometry requires intensive computational processing for annotation of mass spectra and identification of metabolites. Computational analysis tools that are fully integrated with multiple functions and are easily operated by users who lack extensive knowledge in programing are needed in this research field...
March 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28326859/performance-evaluation-of-3d-vision-based-semi-autonomous-control-method-for-assistive-robotic-manipulator
#14
Hyun W Ka, Cheng-Shiu Chung, Dan Ding, Khara James, Rory Cooper
We developed a 3D vision-based semi-autonomous control interface for assistive robotic manipulators. It was implemented based on one of the most popular commercially available assistive robotic manipulator combined with a low-cost depth-sensing camera mounted on the robot base. To perform a manipulation task with the 3D vision-based semi-autonomous control interface, a user starts operating with a manual control method available to him/her. When detecting objects within a set range, the control interface automatically stops the robot, and provides the user with possible manipulation options through audible text output, based on the detected object characteristics...
March 22, 2017: Disability and Rehabilitation. Assistive Technology
https://www.readbyqxmd.com/read/28325018/imquant-an-image-based-fluorescence-reader-for-quantitative-lateral-flow-immunoassays
#15
Kaushik Basak Chowdhury, Jayaraj Joseph, Jayaraman Kiruthi Vasan, Mohanasankar Sivaprakasam
Fluorescence immunoassays (FIA) have strong potential in enabling rapid quantitative immunological testing at point of care. Existing state of the art instruments employ laser scanning of FIA test kits, which require the use of electromechanical systems, making the instrument bulky, heavy and less reliable in the long term. There is a growing need for an extremely compact and reliable, motion-free, automated reader for accurate quantification of immunoassays. Here, we present ImQuant, an image based FIA reader with integrated monochromatic excitation source, optical filtering and real time image capture, assisted with an intuitive graphical user interface...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28323114/physician-activity-during-outpatient-visits-and-subjective-workload
#16
Alan Calvitti, Harry Hochheiser, Shazia Ashfaq, Kristin Bell, Yunan Chen, Robert El Kareh, Mark T Gabuzda, Lin Liu, Sara Mortensen, Braj Pandey, Steven Rick, Richard L Street, Nadir Weibel, Charlene Weir, Zia Agha
We describe methods for capturing and analyzing EHR use and clinical workflow of physicians during outpatient encounters and relating activity to physicians' self-reported workload. We collected temporally-resolved activity data including audio, video, EHR activity, and eye-gaze along with post-visit assessments of workload. These data are then analyzed through a combination of manual content analysis and computational techniques to temporally align streams, providing a range of process measures of EHR usage, clinical workflow, and physician-patient communication...
March 17, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28323105/automated-workflows-for-modelling-chemical-fate-kinetics-and-toxicity
#17
José Vicente Sala Benito, Alicia Paini, Andrea-Nicole Richarz, Thorsten Meinl, Michael R Berthold, Mark T D Cronin, Andrew P Worth
Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA)...
March 17, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/28321973/cortical-and-subcortical-mechanisms-of-brain-machine-interfaces
#18
Silvia Marchesotti, Roberto Martuzzi, Aaron Schurger, Maria Laura Blefari, José R Del Millán, Hannes Bleuler, Olaf Blanke
Technical advances in the field of Brain-Machine Interfaces (BMIs) enable users to control a variety of external devices such as robotic arms, wheelchairs, virtual entities and communication systems through the decoding of brain signals in real time. Most BMI systems sample activity from restricted brain regions, typically the motor and premotor cortex, with limited spatial resolution. Despite the growing number of applications, the cortical and subcortical systems involved in BMI control are currently unknown at the whole-brain level...
March 21, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28320671/an-indoor-wayfinding-system-based-on-geometric-features-aided-graph-slam-for-the-visually-impaired
#19
He Zhang, Cang Ye
This paper presents a 6-DOF pose estimation (PE) method and an indoor wayfinding system based on the method for the visually impaired. The PE method involves two graph SLAM processes to reduce the accumulative pose error of the device. In the first step, the floor plane is extracted from the 3D camera's point cloud and added as a landmark node into the graph for 6-DOF SLAM to reduce roll, pitch and Z errors. In the second step, the wall lines are extracted and incorporated into the graph for 3-DOF SLAM to reduce X, Y and yaw errors...
March 15, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28318915/computer-assisted-positioning-of-the-proximal-segment-after-sagittal-split-osteotomy-of-the-mandible-preclinical-investigation-of-a-novel-electromagnetic-navigation-system
#20
Igor Nova, Sebastian Kallus, Moritz Berger, Oliver Ristow, Urs Eisenmann, Christian Freudlsperger, Jürgen Hoffmann, Hartmut Dickhaus
INTRODUCTION: Modifications of the temporomandibular joint position after mandible osteotomy are reluctantly accepted in orthognathic surgery. To tackle this problem, we developed a new navigation system using miniaturized electromagnetic sensors. Our imageless navigation approach is therefore optimized to avoid complications of previously proposed optical approaches such as the interference with established surgical procedures and the line of sight problem. MATERIAL AND METHODS: High oblique sagittal split osteotomies were performed on 6 plastic skull mandibles in a laboratory under conditions comparable to the operating theatre...
February 17, 2017: Journal of Cranio-maxillo-facial Surgery
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