scholarly journals App-based Quantification of Crystal Phases and Amorphous Content in ZIFs Biocomposites

2021 ◽  
Author(s):  
Michael Hafner ◽  
Laura Villanova ◽  
Francesco Carraro
Keyword(s):  
Drug Delivery ◽  
Web Application ◽  
Internal Standard ◽  
Calibration Procedure ◽  
Analysis Tool ◽  
Zeolitic Imidazolate Frameworks ◽  
Structure Property ◽  
Amorphous Content ◽  
Crystal Phases ◽  
Diffraction Patterns

The performance of Zeolitic Imidazolate Frameworks (ZIFs) as protective hosts for proteins in drug delivery or biocatalysis strongly depends on the type of crystalline phases used for the encapsulation of the biomacromolecule (biomacromolecule@ZIF). Therefore, quantifying the different crystal phases, and the amount of amorphous content of ZIFs is becoming increasingly important for a better understanding of the structure-property relationship. Typically, crystalline ZIF phases are qualitatively identified from diffraction patterns. However, accurate phase examinations are time-consuming and require specialized expertise. Here, we propose a calibration procedure (internal standard ZrO2) for the rapid and quantitative analysis of crystalline and amorphous ZIF phases from diffraction patterns. We integrated the procedure into a user-friendly web application, named ZIF Phase Analysis, which facilitates ZIF-based data analysis. As a result, it is now possible to quantify i) the relative amount of various common crystal phases (sodalite, diamondoid, ZIF-CO3-1, ZIF-EC-1, U12 and ZIF-L) in biomacromolecule@ZIF biocomposites based on Zn2+ and 2-methylimidazole (HmlM) and ii) the crystalline-to-amorphous ratio. This new analysis tool will advance the research on ZIF biocomposites for drug delivery and biocatalysis.

Flame ionization detector response to coeluting hydrocarbons and carbon disulphide and its application to the determination of the sum of C6-C11 alkanes and cycloalkanes in air

1983 ◽  
Vol 48 (3) ◽  
pp. 722-734
Author(s):  
Martin Koval
Keyword(s):  
Carbon Disulphide ◽  
Internal Standard ◽  
Calibration Procedure ◽  
Detector Response ◽  
Column Temperature ◽  
Flame Ionization ◽  
Other Substances ◽  
Flame Ionisation Detector ◽  
Ionisation Detector

The flame ionisation detector response to C6-C11 aliphatic hydrocarbon solutions in carbon disulphide in the concentration range between 1.3-9.5 mg ml-1 retained lineary despite the excess of solvent entering the detector simultaneously with the analyte. Pure carbon disulphide exhibited a small positive detector response which did not interfere in calibration procedure and which, under certain GC conditions, inverted to negative values. This response was not proportional to the injected volume and was strongly influenced by the column temperature and/or bleed. On the basis of these findings, a method compatible with the widely used charcoal tube carbon disulphide desorption procedure was developed and evaluated. It consists of static desorption of the sum of aliphatic alkanes and cycloalkanes from the activated charcoal after which an internal standard is added to the supernatant eluate. The resulting carbon disulphide solution is analysed on a highly polar stationary phase 1,2,3-tris(2-cyanoethoxy)propane where the solvent and the analyte coelute in a single peak, the height of which is practically proportional to the sum of alkanes and cycloalkanes present. This also makes determinations of other substances present in the sample more simple. The field test of the proposed method yielded values comparable in precision and accuracy with a control infrared spectrophotometric method.

scholarly journals RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Danying Shao ◽  
Nabeel Ahmed ◽  
Nishant Soni ◽  
Edward P. O’Brien
Keyword(s):  
Integer Programming ◽  
Web Application ◽  
Stop Codon ◽  
Ribosome Profiling ◽  
Programming Method ◽  
Analysis Tool ◽  
Site Location ◽  
Link Type ◽  
Wide Range ◽  
A Site

Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.

scholarly journals The Web Application of Constitution Analysis System - SCAT (Sasang Constitution Analysis Tool) -

2016 ◽  
Vol 28 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Ji-Ho So ◽  
Jang-Woong Kim ◽  
Ji-Ho Nam ◽  
Bum-Ju Lee ◽  
Young-Su Kim ◽  
...  
Keyword(s):  
Web Application ◽  
Analysis Tool ◽  
Sasang Constitution ◽  
Analysis System ◽  
The Web

Sintering AlN Ceramics Below 1500°C with MgO-CaO-Al2O3-SiO2 Glass Addition

2007 ◽  
Vol 336-338 ◽  
pp. 1868-1871 ◽  
Author(s):  
Cheng Fu Yang ◽  
Chien Min Cheng ◽  
Ho Hua Chung ◽  
Chao Chin Chan
Keyword(s):  
Sintering Temperature ◽  
Sol Gel ◽  
X Ray Diffraction ◽  
Dielectric Characteristics ◽  
Sintering Aid ◽  
Glass Addition ◽  
X Ray ◽  
Crystal Phases ◽  
Diffraction Patterns ◽  
Scanning Electron

5~15 wt% MgO-CaO-Al2O3-SiO2 (MCAS, fabricated by sol-gel method) glass is used as the sintering aid of AlN ceramics. The sintering is proceeded from 1350oC~1550oC, scanning electron microscope is used to observe the sintered morphologies and X-ray diffraction pattern are used to confirm the crystal structures. From the SEM observations, as 10wt% and 15wt% MCAS is added, AlN ceramics can be densified at 1500oC and 1450oC, which are much lower than the before studies were. From the X-ray diffraction patterns, the crystal phases of MCAS-AlN ceramics are AlN, Al2O3, and cordierite phases. In this study, the dielectric characteristics of MCAS-AlN ceramics are also developed as a function of MCAS content and sintering temperature.

scholarly journals Peculiarities of the environmental light pollution in Chernivtsi Region

2021 ◽  
pp. 66-75
Author(s):  
А. V. Zhuk ◽  
O. D. Zarochentseva
Keyword(s):  
Web Application ◽  
Industrial Development ◽  
Urban Expansion ◽  
Wildlife Habitat ◽  
Light Pollution ◽  
Analysis Tool ◽  
Night Time ◽  
Data Set ◽  
Rural Landscapes ◽  
Medical Disorders

Introduction. Every year industrial development and economic growth make light pollution worsen on a global scale. It is a well-known fact that artificial outdoor lighting causes destruction of wildlife habitat, impacts circadian rhythms of all living beings, disrupts animal behavior and leads to medical disorders of humans. Over the last decade scientists switched their focus from artificial sky glow over large cities to light pollution of rural landscapes, protected areas and roadways.  The purpose of this paper consists in assessing night-time light emissions over Chernivtsi Region as well as over city of Chernivtsi using satellite measurements. Methods. Measurements of night-time light emissions were obtained with the help of GIS web application Radiance Light Trends and the light trends analysis tool. The application allows examination of changes in light pollution across selected areas since 1992 and performs time-series analysis with fitting an exponential curve into the data set. Results. The trend in light emissions observed by satellites for Chernivtsi Region indicated brightening at the rate of 2.45 % per year from 1992 to 2014, and 2.93 % per year from 2014 to 2021. The marked increase in the intensity of atmospheric light pollution over Chernivtsi Region is largely attributable to urban expansion of district centers, national & international routes and resort complexes. At the same time, the spatial pattern of the light environment over city of Chernivtsi indicated a nearly constant level of aggregate annual light radiance for the last 8 years. A large irregularly shaped "light spot" was detected on the territory of the Prut-Siret interfluve. It crosses the region from the northwest to the southeast and covers the regional center with its suburbs and the national highway H-10. The night light radiance constitutes 47.49∙10-9 mW/cm2 sr in the center of the spot and more than 1∙10-9 mW/cm2 sr at its edges. The highest level of light pollution in Chernivtsi Region was registered in January, and the lowest – in March. Night-time light emission over two most illuminated highways remains relatively constant regardless of the season. Conclusion. The study highlights that despite low population and low economic activity, rural landscapes demonstrate a trend towards increasing brightness of the night sky. The findings provide a quantitative reference for light pollution management in the region and for further research in the area. 

scholarly journals KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 832
Author(s):  
Finn Kuusisto ◽  
Daniel Ng ◽  
John Steill ◽  
Ian Ross ◽  
Miron Livny ◽  
...  
Keyword(s):  
Text Mining ◽  
Web Application ◽  
Biomedical Applications ◽  
Analysis Tool ◽  
Trial And Error ◽  
Web Tool ◽  
Interactive Analysis ◽  
Term List ◽  
Public Resource ◽  
The Web

Many important scientific discoveries require lengthy experimental processes of trial and error and could benefit from intelligent prioritization based on deep domain understanding. While exponential growth in the scientific literature makes it difficult to keep current in even a single domain, that same rapid growth in literature also presents an opportunity for automated extraction of knowledge via text mining. We have developed a web application implementation of the KinderMiner algorithm for proposing ranked associations between a list of target terms and a key phrase. Any key phrase and target term list can be used for biomedical inquiry. We built the web application around a text index derived from PubMed. It is the first publicly available implementation of the algorithm, is fast and easy to use, and includes an interactive analysis tool. The KinderMiner web application is a public resource offering scientists a cohesive summary of what is currently known about a particular topic within the literature, and helping them to prioritize experiments around that topic. It performs comparably or better to similar state-of-the-art text mining tools, is more flexible, and can be applied to any biomedical topic of interest. It is also continually improving with quarterly updates to the underlying text index and through response to suggestions from the community. The web application is available at https://www.kinderminer.org.

scholarly journals CalmBelt: Rapid SARS-CoV-2 Genome Characterization for Outbreak Tracking

2021 ◽  
Vol 8 ◽  
Author(s):  
Hatairat Yingtaweesittikul ◽  
Karrie Ko ◽  
Nurdyana Abdul Rahman ◽  
Shireen Yan Ling Tan ◽  
Niranjan Nagarajan ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Web Application ◽  
Clinical Laboratory ◽  
Clinical Samples ◽  
Analysis Tool ◽  
Whole Genome ◽  
Multiple Use ◽  
Sequencing Technology ◽  
Health Crisis ◽  
Genome Characterization

Background: The ongoing COVID-19 pandemic is a global health crisis caused by the spread of SARS-CoV-2. Establishing links between known cases is crucial for the containment of COVID-19. In the healthcare setting, the ability to rapidly identify potential healthcare-associated COVID-19 clusters is critical for healthcare worker and patient safety. Increasing sequencing technology accessibility has allowed routine clinical diagnostic laboratories to sequence SARS-CoV-2 in clinical samples. However, these laboratories often lack specialized informatics skills required for sequence analysis. Therefore, an on-site, intuitive sequence analysis tool that enables clinical laboratory users to analyze multiple genomes and derive clinically relevant information within an actionable timeframe is needed.Results: We propose CalmBelt, an integrated framework for on-site whole genome characterization and outbreak tracking. Nanopore sequencing technology enables on-site sequencing and construction of draft genomes for multiple SARS-CoV-2 samples within 12 h. CalmBelt's interactive interface allows users to analyse multiple SARS-CoV-2 genomes by utilizing whole genome information, collection date, and additional information such as predefined potential clusters from epidemiological investigations. CalmBelt also integrates established SARS-CoV-2 nomenclature assignments, GISAID clades and PANGO lineages, allowing users to visualize relatedness between samples together with the nomenclatures. We demonstrated multiple use cases including investigation of potential hospital transmission, mining transmission patterns in a large outbreak, and monitoring possible diagnostic-escape.Conclusions: This paper presents an on-site rapid framework for SARS-CoV-2 whole genome characterization. CalmBelt interactive web application allows non-technical users, such as routine clinical laboratory users in hospitals to determine SARS-CoV-2 variants of concern, as well as investigate the presence of potential transmission clusters. The framework is designed to be compatible with routine usage in clinical laboratories as it only requires readily available sample data, and generates information that impacts immediate infection control mitigations.

scholarly journals Firing transformations of an argentinean calcareous commercial clay

Cerâmica ◽  
2013 ◽  
Vol 59 (350) ◽  
pp. 254-261 ◽  
Author(s):  
M. F. Serra ◽  
M.S. Conconi ◽  
G. Suarez ◽  
E. F. Agietti ◽  
N. M. Rendtorff
Keyword(s):  
Internal Standard ◽  
Ceramic Materials ◽  
Thermal Treatments ◽  
Quartz Content ◽  
Spinel Type ◽  
Porosity Evolution ◽  
Phase Quantification ◽  
Alumino Silicate ◽  
Diffraction Patterns ◽  
Sintering Characteristics

Mineralogical transformations caused by firing are usually studied by XRD methods only semi-quantitatively. In this work the original mineral disappearance and the neo-mineralization were evaluated quantitatively. Furthermore an indirect non crystalline phase quantification was performed under 1100 ºC was also carried out using the quartz content as internal standard. This study specifically discusses the behavior of an Argentinean white calcareous earthenware commercial when subjected to traditional ceramic firing, besides the technological importance of this particular material, it acts as a model for other clay based ceramic materials. Materials were subjected to thermal treatments between 700 ºC and 1100 ºC. A preliminary sintering characterization was carried out by contraction and porosity evolution. Simultaneous thermogravimetric and differential thermal analysis (TG-DTA) was carried out to elucidate the actual temperature at which the chemical changes occur. Finally, a quantitative analysis based on the Rietveld refinement of the X-ray diffraction patterns was performed to characterize the crystalline phases present in both the clay and in the materials obtained after different thermal treatments. The actual chemical reactions are proposed. The phases identified after firing at traditional working temperature (1040 ºC) are quartz, plagioclase, and the Spinel type alumino-silicate, accompanied by the non-diffracting un-reacted metakaolin and some amount of amorphous glassy phase. At intermediate temperatures (900 ºC) the presence of gehlenite was also detected. The carbonates (calcite and dolomite) presence and decomposition were also evaluated and demonstrated to determine the sintering characteristics of this material.

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