scholarly journals Mining Proteome Research Reports: A Bird’s Eye View

Proteomes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 29
Author(s):  
Jagajjit Sahu
Keyword(s):  
Programming Languages ◽  
Scientific Data ◽  
Scale Analysis ◽  
Medical Subject Headings ◽  
Publication Trends ◽  
Weighted Degree ◽  
Systematic Analysis ◽  
Analytical Approaches ◽  
Weighted Degree Centrality ◽  
Unique Genes

The complexity of data has burgeoned to such an extent that scientists of every realm are encountering the incessant challenge of data management. Modern-day analytical approaches with the help of free source tools and programming languages have facilitated access to the context of the various domains as well as specific works reported. Here, with this article, an attempt has been made to provide a systematic analysis of all the available reports at PubMed on Proteome using text mining. The work is comprised of scientometrics as well as information extraction to provide the publication trends as well as frequent keywords, bioconcepts and most importantly gene–gene co-occurrence network. Out of 33,028 PMIDs collected initially, the segregation of 24,350 articles under 28 Medical Subject Headings (MeSH) was analyzed and plotted. Keyword link network and density visualizations were provided for the top 1000 frequent Mesh keywords. PubTator was used, and 322,026 bioconcepts were able to extracted under 10 classes (such as Gene, Disease, CellLine, etc.). Co-occurrence networks were constructed for PMID-bioconcept as well as bioconcept–bioconcept associations. Further, for creation of subnetwork with respect to gene–gene co-occurrence, a total of 11,100 unique genes participated with mTOR and AKT showing the highest (64) number of connections. The gene p53 was the most popular one in the network in accordance with both the degree and weighted degree centrality, which were 425 and 1414, respectively. The present piece of study is an amalgam of bibliometrics and scientific data mining methods looking deeper into the whole scale analysis of available literature on proteome.

scholarly journals General Analytical Schemes for the Characterization of Pectin-Based Edible Gelled Systems

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Maryam Haghighi ◽  
Karamatollah Rezaei
Keyword(s):  
Image Analysis ◽  
Three Dimensional ◽  
Analytical Techniques ◽  
Physicochemical Analysis ◽  
Visual Observation ◽  
Scientific Data ◽  
Rheological Measurement ◽  
Rheological Measurements ◽  
Analytical Approaches

Pectin-based gelled systems have gained increasing attention for the design of newly developed food products. For this reason, the characterization of such formulas is a necessity in order to present scientific data and to introduce an appropriate finished product to the industry. Various analytical techniques are available for the evaluation of the systems formulated on the basis of pectin and the designed gel. In this paper, general analytical approaches for the characterization of pectin-based gelled systems were categorized into several subsections including physicochemical analysis, visual observation, textural/rheological measurement, microstructural image characterization, and psychorheological evaluation. Three-dimensional trials to assess correlations among microstructure, texture, and taste were also discussed. Practical examples of advanced objective techniques including experimental setups for small and large deformation rheological measurements and microstructural image analysis were presented in more details.

scholarly journals Competitive Conditions in Global Value Chain Networks: An Assessment Using Entropy and Network Analysis

Entropy ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1068 ◽  
Author(s):  
Georgios Angelidis ◽  
Evangelos Ioannidis ◽  
Georgios Makris ◽  
Ioannis Antoniou ◽  
Nikos Varsakelis
Keyword(s):  
Value Chain ◽  
Value Added ◽  
Value Chains ◽  
Global Value Chain ◽  
Degree Centrality ◽  
Sector Structure ◽  
Input Output ◽  
Weighted Degree ◽  
The World ◽  
Weighted Degree Centrality

We investigated competitive conditions in global value chains (GVCs) for a period of fifteen years (2000–2014), focusing on sector structure, countries’ dominance and diversification. For this purpose, we used data from the World Input–Output Database (WIOD) and examined GVCs as weighted directed networks, where countries are the nodes and value added flows are the edges. We compared the in-and out-weighted degree centralization of the sectoral GVC networks in order to detect the most centralized, on the import or export side, respectively (oligopsonies and oligopolies). Moreover, we examined the in- and out-weighted degree centrality and the in- and out-weight entropy in order to determine whether dominant countries are also diversified. The empirical results reveal that diversification (entropy) and dominance (degree) are not correlated. Dominant countries (rich) become more dominant (richer). Diversification is not conditioned by competitiveness.

scholarly journals Testing the precautionary argument after the Lucky Dragon incident

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Matthias Dörries
Keyword(s):  
Scientific Reasoning ◽  
Scientific Data ◽  
Asia Pacific ◽  
Historical Study ◽  
Historical Case Study ◽  
Historical Case ◽  
Systematic Analysis ◽  
Content Type ◽  
The 1950S ◽  
Energy Argument

PurposeThis paper uses a historical case study, the controversy over the possibility of climatic extremes caused by hydrogen bomb tests on Pacific Ocean atolls during the 1950s, to show how, in a context of few scientific data and high uncertainty, political affiliations and public concerns shaped two types of argumentation, the “energy” and the “precautionary” arguments.Design/methodology/approachSystematic analysis of publications 1954–1956: scientific and semiscientific articles, publications of C.-N. Martin and contemporary newspaper articles, especially from the Asia–Pacific region.FindingsFirst, epistemological and scientific reasoning about the likelihood of extreme natural events aligned to political convictions and pressure. Second, a geographical and social distribution of arguments: the relativizing “energy argument” prevailed in English-language scientific journals, while the “precautionary argument” dominated in popular journals and newspapers published worldwide. Third, while the “energy argument” attained general scientific consensus within two years, it lost out in the long run. The proponents of the “precautionary argument” raised relevant research questions that, though first rejected in the 1950s, later exposed the fallacies of the “energy argument” (shown for the case of the climatologist William W. Kellogg).Originality/valueIn contrast to the existing secondary literature, this paper presents a balanced view of the weaknesses and strengths of two lines of arguments in the 1950s. Further, this historical study sheds light on how once-discarded scientific theories may ultimately be reconsidered in a completely different political and scientific context, thus justifying the original precautionary argument.

scholarly journals From Genome to Function: Systematic Analysis of the Soil BacteriumBacillus subtilis

2001 ◽  
Vol 2 (1) ◽  
pp. 22-24 ◽  
Author(s):  
Colin R. Harwood ◽  
Samuel G. Crawshaw ◽  
Anil Wipat
Keyword(s):  
Functional Analysis ◽  
Bacillus Subtilis ◽  
Genome Sequence ◽  
Water Sources ◽  
Natural Environments ◽  
Positive Bacterium ◽  
Systematic Analysis ◽  
Analysis Programme ◽  
Analytical Approaches

Bacillus subtilisis a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of theB. subtilisgenome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression ofBacillusgenesin situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere.

Pore-scale analysis of formation damage; A review of existing digital and analytical approaches

2021 ◽  
Vol 288 ◽  
pp. 102345
Author(s):  
Mahmoud Rezaeizadeh ◽  
Seyed Hasan Hajiabadi ◽  
Hamed Aghaei ◽  
Martin J. Blunt
Keyword(s):  
Formation Damage ◽  
Scale Analysis ◽  
Pore Scale ◽  
Analytical Approaches

scholarly journals How exploring Python can level up your data visualization

2021 ◽  
Author(s):  
Annabel Cansdale
Keyword(s):  
Data Analysis ◽  
Learning Curve ◽  
Programming Languages ◽  
Data Visualization ◽  
Graphical Representation ◽  
Scientific Data ◽  
Scientific World ◽  
Invaluable Tool ◽  
Dataset Size ◽  
Scientific Data Visualization

Data visualization, i.e., the graphical representation of data, is a vital skill for every scientist to develop – aiding with the interpretation of data and providing an accessible way to communicate these data with others. In the scientific world, data visualization is used to produce eye-catching figures to share results with peers and the wider community. While these visualizations are achievable using no coding, they can be restricted by the dataset size, plotting style and overall cost of the software. Learning to code solves many of these issues and while the learning curve remains a barrier to use, programming is becoming a must-have skill in many fields. Python is one of the world’s most popular programming languages and is at the forefront of data analysis and visualization, producing clear, engaging and reproducible figures in all manner of styles. As biological datasets increase in size and number, the reproducibility and flexibility of Python result in an invaluable tool for scientific data visualization. This article will introduce the use of Python for data visualization and provide some guidance on how to get started.

scholarly journals Reviewing the Past to Inform the Future: A Literature Review of Social Media in Tourism

2018 ◽  
Vol 7 (2) ◽  
pp. 115-131 ◽  
Author(s):  
Zohreh Zara Zarezadeh ◽  
H. Raymond Rastegar ◽  
Ulrike Gretzel
Keyword(s):  
Social Media ◽  
Literature Review ◽  
User Generated Content ◽  
Future Research ◽  
Publication Trends ◽  
Systematic Analysis ◽  
Tourism Research ◽  
The Past ◽  
Research Designs ◽  
Consumer Perspective

Abstract Acknowledging the significant advancement of social media, the role and impact of social media has been widely discussed in tourism research. As a result, it has become increasingly difficult to obtain an overview of the knowledge produced in relation to the topic. Review studies provide such overviews to guide future research efforts. This study reviews and analyses 152 tourism-related social media publications since 2008. Based on a qualitative systematic analysis of publications that address the topic from a consumer perspective, the paper identifies publication trends and highlights patterns in the topics, aims, and research designs of existing publications. Specifically, it captures a broader array of consumer-centric topics than previous reviews and highlights methodological gaps. Moreover, the research argues that there is still ample room for more research on social media in tourism, particularly as the existing literature neglects social media beyond review platforms while demonstrating that user-generated content greatly influences tourist behaviours and experiences.

scholarly journals Disk failures in the EOS setup at CERN

2019 ◽  
Vol 214 ◽  
pp. 04046
Author(s):  
Dirk Duellmann ◽  
Alfonso Portabales
Keyword(s):  
Machine Learning ◽  
Scientific Data ◽  
End User ◽  
Systematic Analysis ◽  
Repair Costs ◽  
Machine Learning Model ◽  
Data Collection And Analysis ◽  
Service Degradation ◽  
Core Service ◽  
Disk Failures

The EOS deployment at CERN is a core service used for both scientific data processing, analysis and as back-end for general end-user storage (eg home directories/CERNBOX). The collected disk failure metrics over a period of 1 year from a deployment size of some 70k disks allows a first systematic analysis of the behaviour of different hard disk types for the large CERN usecases. In this contribution we describe the data collection and analysis, summarise the measured rates and compare them with other large disk deployments. We further describe initial steps to use the collected failure and SMART metrics to develop a machine learning model predicting imminent failures and hence avoid service degradation and repair costs.

A Systematic Review of API Evolution Literature

2022 ◽  
Vol 54 (8) ◽  
pp. 1-36
Author(s):  
Maxime Lamothe ◽  
Yann-Gaël Guéhéneuc ◽  
Weiyi Shang
Keyword(s):  
Programming Languages ◽  
Research Evaluation ◽  
State Of The Art ◽  
Publication Trends ◽  
Current State ◽  
Software Artifact ◽  
Application Programming ◽  
New Challenges ◽  
The Impact ◽  
Programming Interfaces

Recent software advances have led to an expansion of the development and usage of application programming interfaces (APIs). From millions of Android packages (APKs) available on Google Store to millions of open-source packages available in Maven, PyPI, and npm, APIs have become an integral part of software development. Like any software artifact, software APIs evolve and suffer from this evolution. Prior research has uncovered many challenges to the development, usage, and evolution of APIs. While some challenges have been studied and solved, many remain. These challenges are scattered in the literature, which hides advances and cloaks the remaining challenges. In this systematic literature review on APIs and API evolution, we uncover and describe publication trends and trending topics. We compile common research goals, evaluation methods, metrics, and subjects. We summarize the current state-of-the-art and outline known existing challenges as well as new challenges uncovered during this review. We conclude that the main remaining challenges related to APIs and API evolution are (1) automatically identifying and leveraging factors that drive API changes, (2) creating and using uniform benchmarks for research evaluation, and (3) understanding the impact of API evolution on API developers and users with respect to various programming languages.

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