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Visualization and System Diagrams

James Scott-Brown, Antonis Papachristodoulou
We present sbml-diff, a tool that is able to read a model of a biochemical reaction system in SBML format and produce a range of diagrams showing a range of levels of detail. Each diagram type can be used to visualise a single model, or to visually compare two or more models. The default view depicts species as ellipses, reactions as rectangles, rules as parallelograms, and events as diamonds. A cartoon view replaces the symbols used for reactions based on the associated SBO term (if present). An abstract view represents species as ellipses, and draws edges between these to indicate whether a species increases or decreases the production or degradation of another species...
December 30, 2016: ACS Synthetic Biology
Elisa Parra, Pablo Hervella, David Needham
The material properties of micro- and nanoparticles are fundamental for their bulk properties in suspension, like their stability and encapsulation efficiency. A particularly interesting system with potential biomedical applications is the encapsulation of hydrophobic porphyrins into lipid particles and their use as metal atom chelators, where retention and stability are keys for the design process. The overall goal here was to study the solubility, phase behavior and mixing of octaethylporphyrin (OEP) and OEP-Cu chelates with two core materials, triolein (TO) and cholesteryl acetate (CA), as single microparticles...
December 9, 2016: Journal of Pharmaceutical Sciences
Tim Dwyer
The transformation of data into visuals that are as effective and engaging as possible for compelling presentation is an emerging topic in information visualization research. With this goal in mind, several data-analysis system approaches offer a higher-order network visualization that map insights rather than raw data. Knowledge visualization or externalization in the form of small, focused diagrams can communicate insights as well as help analysts structure their reasoning process.
November 2016: IEEE Computer Graphics and Applications
Cuize Yao, Shiting Yu, Xiuqing Li, Ze Wu, Jiajie Liang, Qiangqiang Fu, Wei Xiao, Tianjiu Jiang, Yong Tang
Here, we describe the development of a triangular silver nanoprism (AgNPR) etching-based plasmonic ELISA for the colorimetric determination of Cr(III) levels in environmental water samples. This involved the creation of a novel signal generation system (substrate reaction solution) for a competitive ELISA in which hydrogen peroxide (H2O2) is used to etch triangular AgNPRs, inducing a change in color. This is achieved by controlling the H2O2 concentration that remains after degradation by catalase, which is conjugated to the secondary antibody of the ELISA...
November 22, 2016: Analytical and Bioanalytical Chemistry
Bowen Yu, Claudio T Silva
Data flow systems allow the user to design a flow diagram that specifies the relations between system components which process, filter or visually present the data. Visualization systems may benefit from user-defined data flows as an analysis typically consists of rendering multiple plots on demand and performing different types of interactive queries across coordinated views. In this paper, we propose VisFlow, a web-based visualization framework for tabular data that employs a specific type of data flow model called the subset flow model...
January 2017: IEEE Transactions on Visualization and Computer Graphics
Yijun Wang, Xiaogang Chen, Xiaorong Gao, Shangkai Gao
This paper presents a benchmark steady-state visual evoked potential (SSVEP) dataset acquired with a 40-target brain-computer interface (BCI) speller. The dataset consists of 64-channel Electroencephalogram (EEG) data from 35 healthy subjects (8 experienced and 27 naïve) while they performed a cue-guided target selecting task. The virtual keyboard of the speller was composed of 40 visual flickers, which were coded using a joint frequency and phase modulation (JFPM) approach. The stimulation frequencies ranged from 8Hz to 15...
November 10, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
Jaimie McGlashan, Michael Johnstone, Doug Creighton, Kayla de la Haye, Steven Allender
Causal loop diagrams developed by groups capture a shared understanding of complex problems and provide a visual tool to guide interventions. This paper explores the application of network analytic methods as a new way to gain quantitative insight into the structure of an obesity causal loop diagram to inform intervention design. Identification of the structural features of causal loop diagrams is likely to provide new insights into the emergent properties of complex systems and analysing central drivers has the potential to identify leverage points...
2016: PloS One
Lukas K Schoenenberger, Steffen Bayer, John P Ansah, David B Matchar, Rajagopal L Mohanavalli, Sean Sw Lam, Marcus Eh Ong
OBJECTIVES: Emergency Department crowding is a serious and international health care problem that seems to be resistant to most well intended but often reductionist policy approaches. In this study, we examine Emergency Department crowding in Singapore from a systems thinking perspective using causal loop diagramming to visualize the systemic structure underlying this complex phenomenon. Furthermore, we evaluate the relative impact of three different policies in reducing Emergency Department crowding in Singapore: introduction of geriatric emergency medicine, expansion of emergency medicine training, and implementation of enhanced primary care...
2016: SAGE Open Medicine
Trivikram Nallamilli, Srikanth Ragothaman, Madivala G Basavaraj
In this study we explore the self assembly of oppositely charged latex particles at decane water interfaces. Two spreading protocols have been proposed in this context. In the first method oppositely charged particles are mixed prior to spreading at the interface, this is called "premixed-mixtures". In the second protocol negatively charged particles are first spread at the interface at known coverage followed by spreading positively charged particles at known coverage and this is called "sequential-mixtures"...
January 15, 2017: Journal of Colloid and Interface Science
Saroj Jayasinghe
Clinicians often encounter patients having complex clinical scenarios (CCS) where diverse and dynamic diagnostic and therapeutic issues interact. A limited range of bedside methods are available to describe such patients and most often it is a diagnostic summary, a problem list, or a list of differential diagnoses. These methods fail to portray the interconnected nature of CCCs. They prevent visualization of a system of networks or a web of causation operative in CCSs.A more holistic conceptualization is required and the author argues for an approach based on systems science...
October 10, 2016: BMC Medical Education
Bonhee Chung
Poor subsistence farmers who live in a semi-arid area of northern Ethiopia build irrigation systems to overcome water shortages. However, there is a high risk of malaria transmission when increased standing water provides more favorable habitats for mosquito breeding. This is a serious problem because there are many barriers to malaria control measures and health care systems in the area. Using a causal loop diagram and computer simulations, the author attempted to visually illustrate positive and negative feedbacks between mosquito and human populations in the context of Simret, which is a small village located in northern Ethiopia and is generally considered a malaria-free area...
August 2016: Korean Journal of Parasitology
Jian Guo, Shuxiang Guo, Yang Yu
In this paper, we proposed a novel master-slave robotic catheterization system with force feedback for VIS (Vascular Interventional Surgery). The force feedback to the operator on the master side is the key factor to improve the safety during VIS. The developed system used the MR (magneto rheological) fluid to realize force feedback, and it used the developed multidimensional monitoring interface to realize the visualization of force feedback, the developed multidimensional monitoring interface can monitor the motion information of the catheter and contact force between catheter tip or side wall and blood vessel wall, and the motion data of the catheter was collected and generated diagram for reference to surgeon...
October 2016: Biomedical Microdevices
Boya Li, Huixia Yang, Yumei Wei, Rina Su, Chen Wang, Wenying Meng, Yongqing Wang, Lixin Shang, Zhenyu Cai, Liping Ji, Yunfeng Wang, Ying Sun, Jiaxiu Liu, Li Wei, Yufeng Sun, Xueying Zhang, Tianxia Luo, Haixia Chen, Lijun Yu
OBJECTIVE: To use Z-scores to compare different charts of femur length (FL) applied to our population with the aim of identifying the most appropriate chart. METHODS: A retrospective study was conducted in Beijing. Fifteen hospitals in Beijing were chosen as clusters using a systemic cluster sampling method, in which 15,194 pregnant women delivered from June 20th to November 30th, 2013. The measurements of FL in the second and third trimester were recorded, as well as the last measurement obtained before delivery...
2016: PloS One
Kyukwang Kim, Hyeong Keun Kim, Hwijoon Lim, Hyun Myung
In this research an open source, low power sensor node was developed to check the growth of mycobacteria in a culture bottle with a nitrate reductase assay method for a drug susceptibility test. The sensor system reports the temperature and color sensor output frequency change of the culture bottle when the device is triggered. After the culture process is finished, a nitrite ion detecting solution based on a commercial nitrite ion detection kit is injected into the culture bottle by a syringe pump to check bacterial growth by the formation of a pigment by the reaction between the solution and the color sensor...
2016: Sensors
Ben C Nolting, Karen C Abbott
When a system has more than one stable state, how can the stability of these states be compared? This deceptively simple question has important consequences for ecosystems, because systems with alternative stable states can undergo dramatic regime shifts. The probability, frequency, duration, and dynamics of these shifts will all depend on the relative stability of the stable states. Unfortunately, the concept of "stability" in ecology has suffered from substantial confusion and this is particularly problematic for systems where stochastic perturbations can cause shifts between coexisting alternative stable states...
April 2016: Ecology
Cord Spreckelsen, Klaus Kabino
BACKGROUND: Gaining overview on a biomedical field of research becomes challenging due to the increasing amount of publications. Computer-supported discourse analysis based on bibliometric data could help scientists to identify focal points and trends. OBJECTIVES: The project aimed at implementing an automatic processing pipeline starting from a PubMed query and leading to a suitable visualization of the thematic evolution of a domain fostering meaningful interpretation...
2016: Studies in Health Technology and Informatics
Natáli Valim Oliver Bento-Torres, Anderson Raiol Rodrigues, Maria Izabel Tentes Côrtes, Daniela Maria de Oliveira Bonci, Dora Fix Ventura, Luiz Carlos de Lima Silveira
We have used the Farnsworth-Munsell 100-hue (FM 100) test and Mollon-Reffin (MR) test to evaluate the colour vision of 93 subjects, 30.4 ± 9.7 years old, who had red-green congenital colour vision deficiencies. All subjects lived in Belém (State of Pará, Brazil) and were selected by the State of Pará Traffic Department. Selection criteria comprised the absence of visual dysfunctions other than Daltonism and no history of systemic diseases that could impair the visual system performance. Results from colour vision deficient were compared with those from 127 normal trichromats, 29...
2016: PloS One
João V Fontana, Hermes Gadêlha, José A Miranda
Elastic fingering supplements the already interesting features of the traditional viscous fingering phenomena in Hele-Shaw cells with the consideration that the two-fluid separating boundary behaves like an elastic membrane. Sophisticated numerical simulations have shown that under maximum viscosity contrast the resulting patterned shapes can exhibit either finger tip-splitting or side-branching events. In this work, we employ a perturbative mode-coupling scheme to get important insights into the onset of these pattern formation processes...
March 2016: Physical Review. E
N Li, D D Li, Y Z Zhang, Y Z Yuan, H Geng, L Xiong, D L Liu
Lipase-producing bacteria are naturally-occurring, industrially-relevant microorganisms that produce lipases, which can be used to synthesize biodiesel from waste oils. The efficiency of lipase expression varies between various microbial strains. Therefore, strains that can produce lipases with high efficiency must be screened, and the conditions of lipase metabolism and optimization of the production process in a given environment must be thoroughly studied. A high efficiency lipase-producing strain was isolated from the sediments of Jinsha River, identified by 16S rRNA sequence analysis as Serratia marcescens, and designated as HS-L5...
March 18, 2016: Genetics and Molecular Research: GMR
Casey M Schneider-Mizell, Stephan Gerhard, Mark Longair, Tom Kazimiers, Feng Li, Maarten F Zwart, Andrew Champion, Frank M Midgley, Richard D Fetter, Stephan Saalfeld, Albert Cardona
Neuronal circuit mapping using electron microscopy demands laborious proofreading or reconciliation of multiple independent reconstructions. Here, we describe new methods to apply quantitative arbor and network context to iteratively proofread and reconstruct circuits and create anatomically enriched wiring diagrams. We measured the morphological underpinnings of connectivity in new and existing reconstructions of Drosophila sensorimotor (larva) and visual (adult) systems. Synaptic inputs were preferentially located on numerous small, microtubule-free 'twigs' which branch off a single microtubule-containing 'backbone'...
March 18, 2016: ELife
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