71 research outputs found
Computational Tools for Hydrogen–Deuterium Exchange Mass Spectrometry Data Analysis
No full textHydrogen-deuterium exchange (HDX) has become a pivotal method for investigating the structural and dynamic properties of proteins. The versatility and sensitivity of mass spectrometry (MS) made the technique the ideal companion for HDX, and today HDX-MS is addressing a growing number of applications in both academic research and industrial settings. The prolific generation of experimental data has spurred the concurrent development of numerous computational tools, designed to automate parts of the workflow while employing different strategies to achieve common objectives. Various computational methods are available to perform automated peptide searches and identification; different statistical tests have been implemented to quantify differences in the exchange pattern between two or more experimental conditions; alternative strategies have been developed to deconvolve and analyze peptides showing multimodal behavior; and different algorithms have been proposed to computationally increase the resolution of HDX-MS data, with the ultimate aim to provide information at the level of the single residue. This review delves into a comprehensive examination of the merits and drawbacks associated with the diverse strategies implemented by software tools for the analysis of HDX-MS data
PyHDX
No full textChanges:
Added ΔRFU in web interface
Fixed bug where duplicate entries appeared in controls by using corrected start and end fields
Initial guesses are now interpolated at fitting function and guesses are now broadcast over sample axis
Added MultiTransform which takes multiple sources as input and SelectTransform for the protein view (3d21e4d70a96cc686a085a2ed0fc21c085fa5463)
Reverted template back to GoldenTemplate #249
Fixed initial guesses by association model (fbe9c23dadc31a2966afd115b7e0b1d9a25d898a)
Added PDBeMolstar protein viewer #252
Minor tweaks to web app css #254If you use this software, please cite it as below
PyHDX
No full text<h3>Features</h3>
<ul>
<li>Integrates with <code>hdxms-datasets</code>, allows public dataset loading from web interface (#327)</li>
</ul>
<h3>Fixes</h3>
<ul>
<li>Fixed RFU app file input, improvements to web app peptide input (#318 )</li>
<li>Fixed changing norms after plotting linear bars (e86bf4ddf3f4b75bdfae0bbab6b85f9f2ee2ca3c)</li>
<li>Various minor fixes</li>
</ul>
<h3>Dependencies</h3>
<ul>
<li>Switched to <code>proplot == 0.9.7</code> version requirement.</li>
</ul>
<h3>Deprecations</h3>
<ul>
<li>Removed the <code>Protein</code> object (#315).</li>
</ul>
<h3>Packaging and distribution:</h3>
<ul>
<li>Switched to hatch for packaging (#331).</li>
<li>Switched to mkdocs for documentation building (#314).</li>
</ul>If you use this software, please cite it as below
MATCH: Disclosing the military city Lisbon
No full textDisclosing the military city Lisbon My project involves a former military site located in the edge of Lisbon. The project is located in the district Beato located near the harbor north of the center of the city. This project is closely related to the studio of Heritage & architecture as it is not only worth keeping, but can and needs to be used to improve the quality of the neighborhood. With this project we find a new use and purpose for the unused site and near urban surroundings. We analyze the area and use this knowledge to create a funded design that shows the quality of the existing and the future. This project is a socially relevant project as it is being redeveloped at this moment by the municipality of Lisbon. A MODERN MANUFACTURING COMPLEX The manufacturing complex is the name for the new purpose of the project. The complex consists out of an upper floor zone with semi-private functions like creative workspaces, schools, conference rooms, hotel, craft brewery and winery. The ground floor is a public area with public spaces, craft shops and a museum. The area can be used by local inhabitants, young skilled entrepreneurs and eventually tourists. The site has zones where the different target groups can conduct their daily activities. The upper part will offer contemporary housing for new users. THE MEETING SPOT The focus of the design is in and around the old warehouse. This area is a meeting spot where all users and target groups can come together and enjoy and experience the qualities of the complex. This area is focused on recreational and cultural activities like a market square, exposition spaces, a food hall, tasting rooms, sport center and activity center. This area is the main entrance of the enclosed complex. This results in a design that is the mediator between the outside world and the manufacturing complex. MATCH The old warehouse has a new public use. This building located in the meeting spot is an old building with a new purpose where the old can be seen, touched and experienced. The focus of the building design is on the relation with the surroundings, the strength of the building characteristics and the relation between old and new. THEMES The project has focused on the problem statement translated into the research question ‘How can an enclosed industrial area work together with the urban surroundings as a tool to become reconnected that will serve as an incubator for future developments?’ With the help of themes the project uses the existing to create a new purpose without losing the values and character of the site. The themes are input for the design strategy and concept. The following themes related to the heritage studio are determined. The main theme ‘unite‘ is overarching social related. Bringing together different target group by promoting social cohesion on site. A new purpose is needed for the complex, but this might have negative consequences like gentrification.Disclosing the military city LisbonDocomomo internationalArchitecture, Urbanism and Building Sciences | Heritage & Architectur
A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization
No full textIntramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with 'self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard
Material stocks and flows in the circular economy: a prospective material flow analysis for vehicles in the Netherlands for 2000-2050
No full textTo allow society to operate within planetary boundaries, it is essential to reduce primary material consumption. The Dutch government has set goals to limit the primary extraction by half in 2030 and to be a fully circular economy by 2050. To be able to achieve this without reducing our standards of living, the only way is to extract the materials we need from the urban mine. Knowledge of the urban mine for the vehicles in our society is incomplete, and this research aims to contribute by studying the material stocks and flows for the most important road, rail, air, and water vehicles by weight in the Netherlands. An inventory is made for the materials in these vehicles between 2000 and 2017, and several sustainable transportation developments are identified which influence the material composition: (i) vehicle electrification, (ii) more effective utilisation of the vehicle fleet, (iii) lifespan elongation for vehicles, (iv) capacity enlargement of vehicles, and (v) modal shift towards low emission modes of transportation. These developments are categorised according to typologies from socio-technical transitions analysis which allow for the quantitative results to be placed in a socio-technical context and to be better interpreted. These ’transition pathways’ are then compared to a reference pathway. Bottom-up, stock-driven, prospective, dynamic material flow analysis was conducted based on exogenous driving factors describing the required transportation service for passenger-, freight-, sea- and air transportation in passenger-kilometres and ton-kilometres. These driving factors were based on the WLO-low projections for the future of Dutch transportation. Outflow was modelled using Weibull distributions based on statistical data for the demographics of vehicles. The historical stock of materials in vehicles in the Netherlands was found to have grown from 28 megatons in 2000 to 36.3 megatons in 2017. Ships contribute two thirds to total mass, cars a quarter, and the rest is in order of reducing mass: road utility vehicles, bicycles, transit vehicles, and aircraft. Ferrous metals contribute most to the total mass (82%) followed by Polymers (5.6%), Copper (3.4%), and Aluminium (3.4%). A small but important contribution is made by Critical Raw Materials, which only contribute 0.8% but the total mass of 74 thousand tons is significant. Of all studied developments, lifespan elongation reduces the primary material demand most by around 40% and the available material from the urban mine, but vehicle stock size is not influenced. Improving the effective utilisation of vehicles does reduce the stock size significantly (by 20%) and primary material demand is reduced by 35%, whilst the amount of material available from the urban mine is reduced by only 10%. Electrification of the vehicle fleet and vehicle capacity enlargement increases the vehicle stock mass by 11% because of the introduction of heavier vehicles. The primary material demand increases strongly by 43% and the materials available from the urban mine are increased by 35%. Important steps required to continue to develop the understanding of the urban mine for the circular economy, are to interpret which proportion of the material outflows are available for reuse, and for which parts of the inflows secondary materials can replace primary materials. Other important objectives are to expand the knowledge for material content of objects in society, and the knowledge on the lifespan of materials and objects in society, because these limit the interpretation of the results the most.https://github.com/grimelda/urmive Repository link Repository of thesis researchIndustrial Ecolog
Mission Planning for Deep Sea Robots
No full textOur challenge was to define a format for a mission plan, and develop an application which allows the users of the robot to create a mission plan effectively. This application should assist the user in the process of creating a mission plan as much as possible. Our client was Allseas who was already the sponsor of the LOBSTER project. During the research phase we learned that our application would be best suited for an offline environment, as the user would not necessarily have an internet connection due to being at sea. Furthermore, we learned that the application had to be easy to use and not too complex. Throughout the course of this project we worked with Scrum, our repository was hosted on GitHub, with Travis CI integrated to test our code. Using this we could see our coverage and errors could not enter our final product. In our team we cooperated with an open culture to prevent frustrations. We made agreements on work hours and software methodologies. Still, we faced challenges which ranged from underestimating time needed for certain features to an increasing complexity of code and data gathering. The final product is a web application which can be accessed offline. This application can be successfully used to create missions for Autonomous Underwater Vehicles, which we showed in our final usability evaluation. The LOBSTER team will be using our product to plan their missions in the future. However, before it can be fully used, the low-level control software of the LOBSTER robots needs to be finished by the LOBSTER team.Bachelor ProjectComputer Science and Engineerin
Cognitive load measurements and stimulated recall interviews for studying the effects of information and communications technology
No full textMany researchers use information and communications technology (ICT)-tools to augment learning in a great variety of tasks. Their effects are generally measured in terms of intended outcomes. This article argues for the use of additional, more general measures to obtain a more complete impression of the effects of ICT-tools. The first study presented in this article shows why tools should not only be studied in terms of their specific intended outcomes, but also in terms of their effects on working memory, and the cognitive mechanisms needed to achieve the intended outcomes. The second study uses cognitive load measurements and stimulated recall interviews to obtain a more comprehensive view of the effects of learning tools. Results suggest that traditional outcome measures need to be complemented with quantitative and qualitative measures of cognitive processes to substantiate conclusions about intended effects of ICT-tools.Technology, Policy and Managemen
Cover Picture: Linking Single‐Molecule Blinking to Chromophore Structure and Redox Potentials (ChemPhysChem 4/2012)
No full textPortable memory consistency for software managed distributed memory in many-core SoC
No full textPorting software to different platforms can require modifications of the application. One of the issues is that the targeted hardware supports another memory consistency model. As a consequence, the completion order of reads and writes in a multi-threaded application can change, which may result in improper synchronization. For example, a processor with out-of-order execution could break synchronization if proper fence instructions are missing. Such a bug can cause sporadic errors, which are hard to debug. This paper presents an approach that makes applications independent of the memory model of the hardware, hence they can be compiled to hardware with any memory architecture. The key is having a memory model that only guarantees the most fundamental orderings of reads and writes, and annotations to specify additional ordering constraints. As a result, tooling can transparently and properly implement fences, cache flushes, etc. when appropriate, without losing flexibility of the hardware design. In a case study, several SPLASH-2 applications are run on a 32-core software cache coherent MicroBlaze system in FPGA. Moreover, this approach also allows mapping to scratch-pad memories and a distributed shared memory architecture
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