scholarly journals SUPPORTING WIDE USER-BASE IN RASTER ANALYSIS – GEOCUBES FINLAND

2018 ◽  
Vol XLII-4 ◽  
pp. 329-334
Author(s):  
L. Lehto ◽  
J. Kähkönen ◽  
J. Oksanen ◽  
T. Sarjakoski
Keyword(s):  
Spatial Analysis ◽  
Large Scale ◽  
Academic Research ◽  
Building Blocks ◽  
Geospatial Analysis ◽  
Research Projects ◽  
Main Building ◽  
Raster Analysis

<p><strong>Abstract.</strong> An initiative has been started in Finland to build a harmonized raster geodata repository, called GeoCubes Finland, to help academic users in carrying out geospatial analysis operations in research projects of diverse disciplines. The aim of the initiative is to expand the adoption of GI methods and tools to new sectors of academic research. GeoCubes Finland is being built in the context of a large-scale program developing national geodata infrastructure for academic studies. The main building blocks of the GeoCubes Finland initiative are: a harmonized, multi-resolution raster geodata storage, a set of standardized mechanisms for accessing the raster contents of the storage, and support facilities for cloud-based geocomputing to help users carry out spatial analysis with the contained datasets.</p>

scholarly journals At close quarters: Combatting Facebook design, features and temporalities in social research

2018 ◽  
Vol 5 (2) ◽  
pp. 205395171880231 ◽  
Author(s):  
Justine Gangneux ◽  
Stevie Docherty
Keyword(s):  
Social Media ◽  
Empirical Data ◽  
Large Scale ◽  
Social Research ◽  
Academic Research ◽  
The Other ◽  
Research Projects ◽  
Social Media Platforms ◽  
Media Research ◽  
Social Media Research

As researchers we often find ourselves grappling with social media platforms and data ‘at close quarters’. Although social media platforms were created for purposes other than academic research – which are apparent in their architecture and temporalities – they offer opportunities for researchers to repurpose them for the collection, generation and analysis of rich datasets. At the same time, this repurposing raises an evolving range of practical and methodological challenges at the small and large scale. We draw on our experiences and empirical data from two research projects, one using Facebook Community Pages and the other repurposing Facebook Activity Logs. This article reflects critically on the specific challenges we faced using these platform features, on their common roots, and the tactics we adopted in response. De Certeau’s distinction between strategy and tactics provides a useful framework for exploring these struggles as located in the practice of doing social research – which often ends up being tactical. This article argues that we have to collectively discuss, demystify and devise tactics to mitigate the strategies and temporalities deeply embedded in platforms, corresponding as far as possible to the temporalities and the aims of our research. Although combat at close quarters is inevitable in social media research, dialogue between researchers is more than ever needed to tip the scales in our favour.

Evaluating Qualitative Research

2017 ◽  
Author(s):  
Jeasik Cho
Keyword(s):  
Qualitative Research ◽  
Large Scale ◽  
Academic Research ◽  
Research Community ◽  
Assessment Tools ◽  
Journal Articles ◽  
Journal Editors ◽  
The Past ◽  
Grant Proposals

This book provides the qualitative research community with some insight on how to evaluate the quality of qualitative research. This topic has gained little attention during the past few decades. We, qualitative researchers, read journal articles, serve on masters’ and doctoral committees, and also make decisions on whether conference proposals, manuscripts, or large-scale grant proposals should be accepted or rejected. It is assumed that various perspectives or criteria, depending on various paradigms, theories, or fields of discipline, have been used in assessing the quality of qualitative research. Nonetheless, until now, no textbook has been specifically devoted to exploring theories, practices, and reflections associated with the evaluation of qualitative research. This book constructs a typology of evaluating qualitative research, examines actual information from websites and qualitative journal editors, and reflects on some challenges that are currently encountered by the qualitative research community. Many different kinds of journals’ review guidelines and available assessment tools are collected and analyzed. Consequently, core criteria that stand out among these evaluation tools are presented. Readers are invited to join the author to confidently proclaim: “Fortunately, there are commonly agreed, bold standards for evaluating the goodness of qualitative research in the academic research community. These standards are a part of what is generally called ‘scientific research.’ ”

scholarly journals Current advances of epigenetics in periodontology from ENCODE project: a review and future perspectives

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Young-Dan Cho ◽  
Woo-Jin Kim ◽  
Hyun-Mo Ryoo ◽  
Hong-Gee Kim ◽  
Kyoung-Hwa Kim ◽  
...  
Keyword(s):  
Large Scale ◽  
Periodontal Diseases ◽  
Research Trends ◽  
Main Body ◽  
Research Projects ◽  
Encode Project ◽  
Dna Elements ◽  
Crucial Information ◽  
Future Direction ◽  
Systemic Health

Abstract Background The Encyclopedia of DNA Elements (ENCODE) project has advanced our knowledge of the functional elements in the genome and epigenome. The aim of this article was to provide the comprehension about current research trends from ENCODE project and establish the link between epigenetics and periodontal diseases based on epigenome studies and seek the future direction. Main body Global epigenome research projects have emphasized the importance of epigenetic research for understanding human health and disease, and current international consortia show an improved interest in the importance of oral health with systemic health. The epigenetic studies in dental field have been mainly conducted in periodontology and have focused on DNA methylation analysis. Advances in sequencing technology have broadened the target for epigenetic studies from specific genes to genome-wide analyses. Conclusions In line with global research trends, further extended and advanced epigenetic studies would provide crucial information for the realization of comprehensive dental medicine and expand the scope of ongoing large-scale research projects.

scholarly journals A Large-Scale COVID-19 Twitter Chatter Dataset for Open Scientific Research—An International Collaboration

Epidemiologia ◽  
2021 ◽  
Vol 2 (3) ◽  
pp. 315-324
Author(s):  
Juan M. Banda ◽  
Ramya Tekumalla ◽  
Guanyu Wang ◽  
Jingyuan Yu ◽  
Tuo Liu ◽  
...  
Keyword(s):  
Large Scale ◽  
Social Dynamics ◽  
Additional Data ◽  
Open Data ◽  
Data Sources ◽  
Research Projects ◽  
Research Groups ◽  
The World ◽  
Data Source

As the COVID-19 pandemic continues to spread worldwide, an unprecedented amount of open data is being generated for medical, genetics, and epidemiological research. The unparalleled rate at which many research groups around the world are releasing data and publications on the ongoing pandemic is allowing other scientists to learn from local experiences and data generated on the front lines of the COVID-19 pandemic. However, there is a need to integrate additional data sources that map and measure the role of social dynamics of such a unique worldwide event in biomedical, biological, and epidemiological analyses. For this purpose, we present a large-scale curated dataset of over 1.12 billion tweets, growing daily, related to COVID-19 chatter generated from 1 January 2020 to 27 June 2021 at the time of writing. This data source provides a freely available additional data source for researchers worldwide to conduct a wide and diverse number of research projects, such as epidemiological analyses, emotional and mental responses to social distancing measures, the identification of sources of misinformation, stratified measurement of sentiment towards the pandemic in near real time, among many others.

scholarly journals Reversed Proteolysis—Proteases as Peptide Ligases

Catalysts ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Peter Goettig
Keyword(s):  
Serine Proteases ◽  
Academic Research ◽  
Building Blocks ◽  
Peptide Bond ◽  
Cysteine Proteases ◽  
Small Peptides ◽  
Natural Peptide ◽  
Peptide Esters ◽  
Natural Amino Acids

Historically, ligase activity by proteases was theoretically derived due to their catalyst nature, and it was experimentally observed as early as around 1900. Initially, the digestive proteases, such as pepsin, chymotrypsin, and trypsin were employed to perform in vitro syntheses of small peptides. Protease-catalyzed ligation is more efficient than peptide bond hydrolysis in organic solvents, representing control of the thermodynamic equilibrium. Peptide esters readily form acyl intermediates with serine and cysteine proteases, followed by peptide bond synthesis at the N-terminus of another residue. This type of reaction is under kinetic control, favoring aminolysis over hydrolysis. Although only a few natural peptide ligases are known, such as ubiquitin ligases, sortases, and legumains, the principle of proteases as general catalysts could be adapted to engineer some proteases accordingly. In particular, the serine proteases subtilisin and trypsin were converted to efficient ligases, which are known as subtiligase and trypsiligase. Together with sortases and legumains, they turned out to be very useful in linking peptides and proteins with a great variety of molecules, including biomarkers, sugars or building blocks with non-natural amino acids. Thus, these engineered enzymes are a promising branch for academic research and for pharmaceutical progress.

scholarly journals A Comprehensive Review: Sphingolipid Metabolism and Implications of Disruption in Sphingolipid Homeostasis

2021 ◽  
Vol 22 (11) ◽  
pp. 5793
Author(s):  
Brianna M. Quinville ◽  
Natalie M. Deschenes ◽  
Alex E. Ryckman ◽  
Jagdeep S. Walia
Keyword(s):  
Nervous System ◽  
Large Scale ◽  
System Development ◽  
Building Blocks ◽  
Cell Types ◽  
Nervous System Development ◽  
Sphingolipid Metabolism ◽  
Lysosomal Storage ◽  
Bioactive Lipids ◽  
Comprehensive Review

Sphingolipids are a specialized group of lipids essential to the composition of the plasma membrane of many cell types; however, they are primarily localized within the nervous system. The amphipathic properties of sphingolipids enable their participation in a variety of intricate metabolic pathways. Sphingoid bases are the building blocks for all sphingolipid derivatives, comprising a complex class of lipids. The biosynthesis and catabolism of these lipids play an integral role in small- and large-scale body functions, including participation in membrane domains and signalling; cell proliferation, death, migration, and invasiveness; inflammation; and central nervous system development. Recently, sphingolipids have become the focus of several fields of research in the medical and biological sciences, as these bioactive lipids have been identified as potent signalling and messenger molecules. Sphingolipids are now being exploited as therapeutic targets for several pathologies. Here we present a comprehensive review of the structure and metabolism of sphingolipids and their many functional roles within the cell. In addition, we highlight the role of sphingolipids in several pathologies, including inflammatory disease, cystic fibrosis, cancer, Alzheimer’s and Parkinson’s disease, and lysosomal storage disorders.

scholarly journals How to manage large-scale collaborative genomics research projects?

2017 ◽  
Vol 25 (5) ◽  
pp. 656-656
Author(s):  
Erinija Pranckevičienė ◽  
Vaidutis Kučinskas
Keyword(s):  
Large Scale ◽  
Research Projects ◽  
Genomics Research

Global scale hydrological modelling at 100 m, 1 h resolution, in Python

2021 ◽  
Author(s):  
Kor de Jong ◽  
Marc van Kreveld ◽  
Debabrata Panja ◽  
Oliver Schmitz ◽  
Derek Karssenberg
Keyword(s):  
Large Scale ◽  
Model Building ◽  
Flow Direction ◽  
Building Blocks ◽  
Global Scale ◽  
Data Availability ◽  
Hydrological Models ◽  
Continental Scale ◽  
Modelling Framework ◽  
Scale Models

&lt;p&gt;Data availability at global scale is increasing exponentially. Although considerable challenges remain regarding the identification of model structure and parameters of continental scale hydrological models, we will soon reach the situation that global scale models could be defined at very high resolutions close to 100 m or less. One of the key challenges is how to make simulations of these ultra-high resolution models tractable ([1]).&lt;/p&gt;&lt;p&gt;Our research contributes by the development of a model building framework that is specifically designed to distribute calculations over multiple cluster nodes. This framework enables domain experts like hydrologists to develop their own large scale models, using a scripting language like Python, without the need to acquire the skills to develop low-level computer code for parallel and distributed computing.&lt;/p&gt;&lt;p&gt;We present the design and implementation of this software framework and illustrate its use with a prototype 100 m, 1 h continental scale hydrological model. Our modelling framework ensures that any model built with it is parallelized. This is made possible by providing the model builder with a set of building blocks of models, which are coded in such a manner that parallelization of calculations occurs within and across these building blocks, for any combination of building blocks. There is thus full flexibility on the side of the modeller, without losing performance.&lt;/p&gt;&lt;p&gt;This breakthrough is made possible by applying a novel approach to the implementation of the model building framework, called asynchronous many-tasks, provided by the HPX C++ software library ([3]). The code in the model building framework expresses spatial operations as large collections of interdependent tasks that can be executed efficiently on individual laptops as well as computer clusters ([2]). Our framework currently includes the most essential operations for building large scale hydrological models, including those for simulating transport of material through a flow direction network. By combining these operations, we rebuilt an existing 100 m, 1 h resolution model, thus far used for simulations of small catchments, requiring limited coding as we only had to replace the computational back end of the existing model. Runs at continental scale on a computer cluster show acceptable strong and weak scaling providing a strong indication that global simulations at this resolution will soon be possible, technically speaking.&lt;/p&gt;&lt;p&gt;Future work will focus on extending the set of modelling operations and adding scalable I/O, after which existing models that are currently limited in their ability to use the computational resources available to them can be ported to this new environment.&lt;/p&gt;&lt;p&gt;More information about our modelling framework is at https://lue.computationalgeography.org.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&lt;p&gt;[1] M. Bierkens. Global hydrology 2015: State, trends, and directions. Water Resources Research, 51(7):4923&amp;#8211;4947, 2015.&lt;br&gt;[2] K. de Jong, et al. An environmental modelling framework based on asynchronous many-tasks: scalability and usability. Submitted.&lt;br&gt;[3] H. Kaiser, et al. HPX - The C++ standard library for parallelism and concurrency. Journal of Open Source Software, 5(53):2352, 2020.&lt;/p&gt;

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