scholarly journals MPTHub: an open-source software for characterizing the transport of particles in biorelevant media

2021 ◽  
Author(s):  
Leandro Gabriel ◽  
Helena Almeida ◽  
Marta Avelar ◽  
Bruno Sarmento ◽  
Jose das Neves
Keyword(s):  
Effective Diffusivity ◽  
Software Tool ◽  
Trajectory Data ◽  
Polystyrene Nanoparticles ◽  
Biorelevant Media ◽  
Time Resolved ◽  
Fundamental Biology ◽  
Living Organisms ◽  
Memory Resources ◽  
User Friendly

The study of the transport of particles in different environments plays an essential role in understanding interactions with humans and other living organisms. Importantly, obtained data can be directly used for multiple applications in fields such as fundamental biology, toxicology or medicine. Particle movement in biorelevant media can be readily monitored using microscopy and converted into time-resolved trajectories using freely available tracking software. However, translation into tangible and meaningful parameters is time-consuming and not always intuitive. Thus, we developed a new software - MPTHub - as an open-access, stand-alone, user-friendly tool for the rapid and reliable analysis of particle trajectories extracted from video microscopy. The software was programmed using Python and allowed to import and analyze trajectory data, and export relevant data such as individual and ensemble time-averaged mean square displacements and effective diffusivity, and anomalous transport exponent. Data processing was reliable, fast (total processing time of less than 10 sec) and required minimal memory resources (up to a maximum of around 150 MB in RAM). Demonstration of software applicability was conducted by studying the transport of different polystyrene nanoparticles (100-200 nm) in mucus surrogates. Overall, MPTHub represents a freely available software tool that can be used even by unexperienced users for studying the transport of particles in biorelevant media.

scholarly journals CHR: An Integrated Software Tool for chilling requirements

2020 ◽  
Author(s):  
Chen Chen ◽  
Wanyu Xu ◽  
Ningning Gou ◽  
Lasu Bai ◽  
Lin Wang ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Software Tool ◽  
Fruit Trees ◽  
Cold Weather ◽  
Chilling Requirements ◽  
Deciduous Fruit ◽  
Heat Requirement ◽  
Integrated Software ◽  
User Friendly ◽  
Analyze Data

Abstract Background Bud dormancy in deciduous fruit trees enables plants to survive cold weather. The buds adopt dormant state and resume growth after satisfying the chilling requirements. Chilling requirements play a key role in flowering time. So far, several chilling models, including ≤ 7.2 °C model, the 0–7.2 °C model, Utah model, and Dynamic Model, have been developed; however, it is still time-consuming to determine the chilling requirements employing any model. This calls for efficient tools that can analyze data. Results In this study, we developed novel software Chilling and Heat Requirement (CHR), by flexibly integrating data conversions, model selection, calculations, statistical analysis, and plotting. Conclusion CHR is a tool for chilling requirements estimation, which will be very useful to researchers. It is very simple, easy, and user-friendly.

Quantification Methods for Construction Waste Generation at Construction Sites: A Review

2010 ◽  
Vol 163-167 ◽  
pp. 4564-4569 ◽  
Author(s):  
Ahmad Firman Masudi ◽  
Che Rosmani Che Hassan ◽  
Noor Zalina Mahmood ◽  
Siti Nazziera Mokhtar ◽  
Nik Meriam Sulaiman
Keyword(s):  
Construction Projects ◽  
Software Tool ◽  
Waste Reduction ◽  
Building Construction ◽  
Civil Infrastructure ◽  
Waste Generation ◽  
Construction Sites ◽  
Construction Waste ◽  
Future Direction ◽  
User Friendly

Estimation of construction and demolition (C&D) waste amount is crucial for implementing waste minimization program. Estimation of C&D waste amount generated is a mean in assessing the potential for waste reduction. Thus, a better understanding of C&D waste generation in terms of causes and sources can be achieved. The aim of this paper is to conduct a review on available construction waste quantification methods from previous studies, which have been utilized in certain countries, while attempting to choose the most suitable and applicable method, and to direct future studies for better quantification methods. This review is applicable only for building construction projects and did not include civil/infrastructure, demolition, renovation, and excavation projects. Six quantification methods and/or waste audit tool available from literatures are discussed, which include their limitation and future direction for this study. It is believed that some combination of these quantification methods could make a good impact in accurate numerical estimation of construction waste amount generated in building construction projects. A strong and accurate database as presented by Soliz-Guzman, combined with effective, vital, and resourceful estimation suggested by Jalali’s Global Index (GI), also with the aid of user-friendly software tool like the SMARTAudit could provide an effective and reliable waste quantification.

scholarly journals NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao Feng ◽  
Evgenii L. Kovrigin ◽  
Carol Beth Post
Keyword(s):  
Kinetic Model ◽  
Molecular Interactions ◽  
Rate Constants ◽  
Nmr Spectra ◽  
Equilibrium Constants ◽  
Software Tool ◽  
Biological Interactions ◽  
Equilibrium Binding ◽  
Accurate Quantitative Analysis ◽  
User Friendly

Abstract The ability of high-resolution NMR spectroscopy to readout the response of molecular interactions at multiple atomic sites presents a unique capability to define thermodynamic equilibrium constants and kinetic rate constants for complex, multiple-step biological interactions. Nonetheless, the extraction of the relevant equilibrium binding and rate constants requires the appropriate analysis of not only a readout that follows the equilibrium concentrations of typical binding titration curves, but also the lineshapes of NMR spectra. To best take advantage of NMR data for characterizing molecular interactions, we developed NmrLineGuru, a software tool with a user-friendly graphical user interface (GUI) to model two-state, three-state, and four-state binding processes. Application of NmrLineGuru is through stand-alone GUIs, with no dependency on other software and no scripted input. NMR spectra can be fitted or simulated starting with user-specified input parameters and a chosen kinetic model. The ability to both simulate and fit NMR spectra provides the user the opportunity to not only determine the binding parameters that best reproduce the measured NMR spectra for the selected kinetic model, but to also query the possibility that alternative models agree with the data. NmrLineGuru is shown to provide an accurate, quantitative analysis of complex molecular interactions.

Targeting the Lowest Concentration of a Toxin That Induces a Detectable Metabolic Response in Living Organisms: Time-Resolved In Vivo 2D NMR during a Concentration Ramp

2020 ◽  
Vol 92 (14) ◽  
pp. 9856-9865
Author(s):  
Daniel Lane ◽  
Wolfgang Bermel ◽  
Paris Ning ◽  
Tae-Yong Jeong ◽  
Richard Martin ◽  
...  
Keyword(s):  
Metabolic Response ◽  
2D Nmr ◽  
Time Resolved ◽  
Living Organisms

Development and Application of Luminescence to Earth and Planetary Sciences: Some Landmarks

2014 ◽  
Vol 357 ◽  
pp. 217-243
Author(s):  
R.H. Biswas
Keyword(s):  
Numerical Models ◽  
Cosmic Ray ◽  
Time Resolved ◽  
Infrared Stimulated Luminescence ◽  
Accuracy And Precision ◽  
Wide Range ◽  
History Of ◽  
Recent Trends ◽  
User Friendly ◽  
Exposure Ages

Luminescence, mainly thermoluminescence (TL) and optically stimulated luminescence (OSL), has been researched for more than five decades towards its application to earth and planetary sciences. Luminescence production mechanism has been understood through several theoretical studies, like analytical kinetic theory, numerical models along with the experimental results. Instrument development has progressed with aim from user friendly TL/OSL reader dedicated for dating to challenging reader forin-situMartian sediment dating. Since the development of optical dating in 1985, the technique revolutionised the research in earth sciences. And since then to recent, many methodologies have been developed and some are in developing stage using different signals, like, single grain OSL, red TL, time resolved OSL, thermally transferred OSL (TT-OSL), post infrared-infrared stimulated luminescence (pIR-IRSL), violet light stimulated luminescence (VSL), infrared radioluminescence (IRRL), etc. with an objective to improve the accuracy and precision and to extend the dating range. The wide range of application in different environment, e.g. aeolian, fluvial, marine, glacier, soil, volcanic materials, heated materials, shocked materials, meteorites, etc. have made the technique successful to understand the quaternary history of earth and planetary information like terrestrial and cosmic ray exposure ages of meteorite, meteoroid orbit, thermal metamorphism history of meteorite etc. The aim of this present paper is to discuss some landmarks and recent trends in the development and application in these areas. Contents of the Paper

scholarly journals Time resolved study of cell death mechanisms induced by amine-modified polystyrene nanoparticles

Nanoscale ◽  
2013 ◽  
Vol 5 (22) ◽  
pp. 10868 ◽  
Author(s):  
Fengjuan Wang ◽  
Mariana G. Bexiga ◽  
Sergio Anguissola ◽  
Patricia Boya ◽  
Jeremy C. Simpson ◽  
...  
Keyword(s):  
Cell Death ◽  
Polystyrene Nanoparticles ◽  
Time Resolved ◽  
Cell Death Mechanisms ◽  
Modified Polystyrene

scholarly journals FlowCal: A User-Friendly, Open Source Software Tool for Automatically Converting Flow Cytometry Data from Arbitrary to Calibrated Units

2016 ◽  
Vol 5 (7) ◽  
pp. 774-780 ◽  
Author(s):  
Sebastian M. Castillo-Hair ◽  
John T. Sexton ◽  
Brian P. Landry ◽  
Evan J. Olson ◽  
Oleg A. Igoshin ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Open Source ◽  
Open Source Software ◽  
Software Tool ◽  
Flow Cytometry Data ◽  
User Friendly

scholarly journals The Role of Proteins in Biosilicification

Scientifica ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-22 ◽  
Author(s):  
Daniel Otzen
Keyword(s):  
Self Assembly ◽  
Organic Matrix ◽  
Specific Protein ◽  
Colloidal Systems ◽  
Protein Properties ◽  
Modified Peptides ◽  
Fundamental Biology ◽  
Living Organisms ◽  
Insight Into

Although the use of silicon dioxide (silica) as a constituent of living organisms is mainly restricted to diatoms and sponges, the ways in which this process is controlled by nature continue to inspire and fascinate. Both diatoms and sponges carry out biosilificiation using an organic matrix but they adopt very different strategies. Diatoms use small and heavily modified peptides called silaffins, where the most characteristic feature is a modulation of charge by attaching long chain polyamines (LCPAs) to lysine groups. Free LCPAs can also cooperate with silaffins. Sponges use the enzyme silicatein which is homologous to the cysteine protease cathepsin. Both classes of proteins form higher-order structures which act both as structural templates and mechanistic catalysts for the polycondensation reaction. In both cases, additional proteins are continuously being discovered which modulate the process further. This paper concentrates on the role of these proteins in the biosilification process as well as in various applications, highlighting areas where focus on specific protein properties may provide further insight. The field of biosilification is a crossroads of different disciplines, where insight into the energetics and mechanisms of molecular self-assembly combine with fundamental biology, complex multicomponent colloidal systems, and an impressive array of potential technological applications.

CellTracker (not only) for dummies

2015 ◽  
Vol 32 (6) ◽  
pp. 955-957 ◽  
Author(s):  
Filippo Piccinini ◽  
Alexa Kiss ◽  
Peter Horvath
Keyword(s):  
Graphical User Interface ◽  
Open Source Software ◽  
Phase Contrast ◽  
Cell Tracking ◽  
Source Code ◽  
Software Tool ◽  
Time Lapse ◽  
Supplementary Information ◽  
Differential Interference Contrast ◽  
User Friendly

Abstract Motivation: Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. Availability and implementation: CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

scholarly journals Brief communication: new perspectives on the calculation of bioaccumulation factors for active substances in living organisms

2020 ◽  
Author(s):  
Aude Ratier ◽  
Christelle Lopes ◽  
Gauthier Multari ◽  
Vanessa Mazerolles ◽  
Patrice Carpentier ◽  
...  
Keyword(s):  
Plant Protection ◽  
Plant Protection Products ◽  
Daily Work ◽  
Bioaccumulation Factors ◽  
On Line ◽  
Living Organisms ◽  
User Friendly ◽  
Data Requirements ◽  
Active Substances ◽  
Test Guideline

AbstractToday, there are no ready-to-use convenient tools in ecotoxicology to diagnose and predict the accumulation and effects of chemical substances on living organisms, accounting for exposure situations that are known to be complex (routes of exposure, metabolization processes, cocktail effects, etc.). Regarding plant protection products in marketing authorization applications, regulation No 283/2013 (EU) defines the data requirements for active substances with a bioaccumulation test on fish according to OECD Test guideline 305. This paper presents new perspectives on the estimation of the bioaccumulation factors via an innovative ready-to-use web tool providing these factors, associated with their uncertainty to facilitate the daily work of regulators, but also of any user, by benefiting of a freely available and user-friendly on-line interface avoiding to invest into underlying mathematical and statistical technicalities. This tool, MOSAICbioacc, is available at https://mosaic.univ-lyon1.fr/bioacc, and can be used by any environmental scientists, ecotoxicologists or managers when accumulation-depuration data are collected and need to be easily and quickly analysed.

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