scholarly journals The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central

2022 ◽  
Vol 8 ◽  
pp. e835
Author(s):  
David Schindler ◽  
Felix Bensmann ◽  
Stefan Dietze ◽  
Frank Krüger
Keyword(s):  
Information Extraction ◽  
Large Scale ◽  
Automated Detection ◽  
Knowledge Graph ◽  
Pubmed Central ◽  
Scientific Methods ◽  
Large Scale Analysis ◽  
Different Types ◽  
Citation Practices

Science across all disciplines has become increasingly data-driven, leading to additional needs with respect to software for collecting, processing and analysing data. Thus, transparency about software used as part of the scientific process is crucial to understand provenance of individual research data and insights, is a prerequisite for reproducibility and can enable macro-analysis of the evolution of scientific methods over time. However, missing rigor in software citation practices renders the automated detection and disambiguation of software mentions a challenging problem. In this work, we provide a large-scale analysis of software usage and citation practices facilitated through an unprecedented knowledge graph of software mentions and affiliated metadata generated through supervised information extraction models trained on a unique gold standard corpus and applied to more than 3 million scientific articles. Our information extraction approach distinguishes different types of software and mentions, disambiguates mentions and outperforms the state-of-the-art significantly, leading to the most comprehensive corpus of 11.8 M software mentions that are described through a knowledge graph consisting of more than 300 M triples. Our analysis provides insights into the evolution of software usage and citation patterns across various fields, ranks of journals, and impact of publications. Whereas, to the best of our knowledge, this is the most comprehensive analysis of software use and citation at the time, all data and models are shared publicly to facilitate further research into scientific use and citation of software.

Situational Breakdowns

2019 ◽  
Author(s):  
Anne Nassauer
Keyword(s):  
United States ◽  
Large Scale ◽  
Contextual Factors ◽  
The United States ◽  
Social Outcomes ◽  
Dynamic Processes ◽  
Collective Decisions ◽  
Different Types ◽  
The Impact

This book provides an account of how and why routine interactions break down and how such situational breakdowns lead to protest violence and other types of surprising social outcomes. It takes a close-up look at the dynamic processes of how situations unfold and compares their role to that of motivations, strategies, and other contextual factors. The book discusses factors that can draw us into violent situations and describes how and why we make uncommon individual and collective decisions. Covering different types of surprise outcomes from protest marches and uprisings turning violent to robbers failing to rob a store at gunpoint, it shows how unfolding situations can override our motivations and strategies and how emotions and culture, as well as rational thinking, still play a part in these events. The first chapters study protest violence in Germany and the United States from 1960 until 2010, taking a detailed look at what happens between the start of a protest and the eruption of violence or its peaceful conclusion. They compare the impact of such dynamics to the role of police strategies and culture, protesters’ claims and violent motivations, the black bloc and agents provocateurs. The analysis shows how violence is triggered, what determines its intensity, and which measures can avoid its outbreak. The book explores whether we find similar situational patterns leading to surprising outcomes in other types of small- and large-scale events: uprisings turning violent, such as Ferguson in 2014 and Baltimore in 2015, and failed armed store robberies.

ON THE CHARACTERISTICS OF INNOVATIVE FIRMS IN KOREA: THE ROLE OF R&D AND INNOVATION TYPE

1999 ◽  
Vol 03 (01) ◽  
pp. 111-131 ◽  
Author(s):  
YONG-TAE PARK ◽  
CHUL-HYUN KIM ◽  
JI-HYO LEE
Keyword(s):  
Large Scale ◽  
Data Gathering ◽  
Policy Implications ◽  
Future Research ◽  
Different Types ◽  
Innovative Firms ◽  
Unexpected Findings ◽  
Innovation Type ◽  
Recent Extension

In spite of the recent extension of our knowledge on technological innovation, little inquiry has been made of the distinctive characteristics between R&D firms and non-R&D firms, as well as between product-innovative firms and process-innovative firms. To this end, the main objective of this empirical study, grounded on a large-scale innovation survey of Korean manufacturing firms, is to contrast these two types of firms. The results were mixed. Some hypotheses were confirmed while others were discordant with expectation. By and large, R&D firms and product-innovative firms seem to share a similar propensity, whereas non-R&D firms and process-innovative firms are alike in character. However, there were some unexpected findings which merit attention and are worthy of in-depth examination. Although the study is subject to limitations in terms of its research design and data gathering, the results render some important policy implications. Furthermore, comparative analyses between different types of innovations need to be addressed more extensively in future research.

scholarly journals A DNA Extraction Protocol from Various Tissues in Woody Species

HortScience ◽  
1997 ◽  
Vol 32 (5) ◽  
pp. 921-922 ◽  
Author(s):  
F.S. Cheng ◽  
S.K. Brown ◽  
N.F. Weeden
Keyword(s):  
Dna Extraction ◽  
Large Scale ◽  
Restriction Analysis ◽  
Woody Species ◽  
Scale Analysis ◽  
Extraction Protocol ◽  
Large Scale Analysis ◽  
Different Types

A DNA extraction protocol was developed for tissues from woody species. DNA was extracted successfully from 11 species and five different types of tissues and was suitable for RAPD and restriction analysis. Spermine precipitation was used to further purify DNA. The protocol can be used for large-scale analysis and mini-preparations.

scholarly journals A Large-scale Analysis of Mixed Initiative in Information-Seeking Dialogues for Conversational Search

2021 ◽  
Vol 39 (4) ◽  
pp. 1-32
Author(s):  
Svitlana Vakulenko ◽  
Evangelos Kanoulas ◽  
Maarten De Rijke
Keyword(s):  
Artificial Intelligence ◽  
Information Seeking ◽  
Large Scale ◽  
Scale Analysis ◽  
Virtual Reference ◽  
Research Areas ◽  
Large Scale Analysis ◽  
Different Types ◽  
Future Data ◽  
Mixed Initiative

Conversational search is a relatively young area of research that aims at automating an information-seeking dialogue. In this article, we help to position it with respect to other research areas within conversational artificial intelligence (AI) by analysing the structural properties of an information-seeking dialogue. To this end, we perform a large-scale dialogue analysis of more than 150K transcripts from 16 publicly available dialogue datasets. These datasets were collected to inform different dialogue-based tasks including conversational search. We extract different patterns of mixed initiative from these dialogue transcripts and use them to compare dialogues of different types. Moreover, we contrast the patterns found in information-seeking dialogues that are being used for research purposes with the patterns found in virtual reference interviews that were conducted by professional librarians. The insights we provide (1) establish close relations between conversational search and other conversational AI tasks and (2) uncover limitations of existing conversational datasets to inform future data collection tasks.

scholarly journals Carotenoids as a Protection Mechanism against Oxidative Stress in Haloferax mediterranei

Antioxidants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1060
Author(s):  
Micaela Giani ◽  
Rosa María Martínez-Espinosa
Keyword(s):  
Oxidative Stress ◽  
Large Scale ◽  
Antioxidant Properties ◽  
Natural Ecosystem ◽  
Haloferax Mediterranei ◽  
Protection Mechanism ◽  
Different Types ◽  
Potential Applications ◽  
Extremophilic Microorganisms

Haloarchaea are extremophilic microorganisms that in their natural ecosystem encounter several sources of oxidative stress. They have developed different strategies to cope with these harsh environmental conditions, among which bacterioruberin production is a very notable strategy. Bacterioruberin (BR) is a C50 carotenoid synthesized in response to different types of stress. Previous works demonstrated that it shows interesting antioxidant properties with potential applications in biotechnology. In this study, Haloferax mediterranei strain R-4 was exposed to different concentrations of the oxidant compound H2O2 to evaluate the effect on carotenoid production focusing the attention on the synthesis of bacterioruberin. Hfx. mediterranei was able to grow in the presence of H2O2 from 1 mM to 25 mM. Cells produced between 16% and 78% (w/v) more carotenoids under the induced oxidative stress compared to control cultures. HPLC-MS analysis detected BR as the major identified carotenoid and confirmed the gradual increase of BR content as higher concentrations of hydrogen peroxide were added to the medium. These results shed some light on the biological role of bacterioruberin in haloarchaea, provide interesting information about the increase of the cellular pigmentation under oxidative stress conditions and will allow the optimization of the production of this pigment at large scale using these microbes as biofactories.

scholarly journals Disrupted core-periphery structure of multimodal brain networks in Alzheimer’s disease

2019 ◽  
Vol 3 (2) ◽  
pp. 635-652 ◽  
Author(s):  
Jeremy Guillon ◽  
Mario Chavez ◽  
Federico Battiston ◽  
Yohan Attal ◽  
Valentina La Corte ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Memory Impairment ◽  
Large Scale ◽  
Brain Connectivity ◽  
Functional Integration ◽  
The Core ◽  
Multiplex Network ◽  
Different Types

In Alzheimer’s disease (AD), the progressive atrophy leads to aberrant network reconfigurations both at structural and functional levels. In such network reorganization, the core and peripheral nodes appear to be crucial for the prediction of clinical outcome because of their ability to influence large-scale functional integration. However, the role of the different types of brain connectivity in such prediction still remains unclear. Using a multiplex network approach we integrated information from DWI, fMRI, and MEG brain connectivity to extract an enriched description of the core-periphery structure in a group of AD patients and age-matched controls. Globally, the regional coreness—that is, the probability of a region to be in the multiplex core—significantly decreased in AD patients as result of a random disconnection process initiated by the neurodegeneration. Locally, the most impacted areas were in the core of the network—including temporal, parietal, and occipital areas—while we reported compensatory increments for the peripheral regions in the sensorimotor system. Furthermore, these network changes significantly predicted the cognitive and memory impairment of patients. Taken together these results indicate that a more accurate description of neurodegenerative diseases can be obtained from the multimodal integration of neuroimaging-derived network data.

scholarly journals Protein interactions and ligand binding: From protein subfamilies to functional specificity

2010 ◽  
Vol 107 (5) ◽  
pp. 1995-2000 ◽  
Author(s):  
Antonio Rausell ◽  
David Juan ◽  
Florencio Pazos ◽  
Alfonso Valencia
Keyword(s):  
Ligand Binding ◽  
Protein Interactions ◽  
Protein Function ◽  
Large Scale ◽  
Protein Families ◽  
Predictive Capacity ◽  
Large Scale Analysis ◽  
Protein Interfaces ◽  
Specificity Determining Positions

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as “specificity determining positions” (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.

scholarly journals The Role of Visual Inspection in the 21st Century

2017 ◽  
Vol 61 (1) ◽  
pp. 262-266 ◽  
Author(s):  
Judi E. See ◽  
Colin G. Drury ◽  
Ann Speed ◽  
Allison Williams ◽  
Negar Khalandi
Keyword(s):  
21St Century ◽  
Visual Inspection ◽  
Past Research ◽  
Vital Role ◽  
Automated Detection ◽  
Lessons Learned ◽  
The Past ◽  
Different Types ◽  
Inspection Process

Visual inspection research has a long history spanning the 20th century and continuing to the present day. Current efforts in multiple venues demonstrate that visual inspection continues to have a vital role for many different types of tasks in the 21st century. The nature of this role spans the range from traditional human visual inspection to fully automated detection of defects. Consequently, today’s practitioners must not only successfully identify and apply lessons learned from the past, but also explore new areas of research in order to derive solutions for modern day issues such as those presented by introducing automation during inspection. A key lesson from past research indicates that the factors that can degrade performance will persist today, unless care is taken to design the inspection process appropriately.

SKU performance and distribution: A large-scale analysis of the role of product characteristics with store scanner data

2021 ◽  
Vol 61 ◽  
pp. 102533
Author(s):  
Martin Hirche ◽  
Luke Greenacre ◽  
Magda Nenycz-Thiel ◽  
Simone Loose ◽  
Larry Lockshin
Keyword(s):  
Large Scale ◽  
Scale Analysis ◽  
Scanner Data ◽  
Product Characteristics ◽  
Large Scale Analysis

scholarly journals Predicting Vaccine Uptake during COVID-19 Crisis: A Motivational Approach

2021 ◽  
Author(s):  
Mathias Schmitz ◽  
Olivier Luminet ◽  
Olivier Klein ◽  
Sofie Morbée ◽  
Omer Van den Bergh ◽  
...  
Keyword(s):  
Risk Perception ◽  
Large Scale ◽  
Autonomous Motivation ◽  
Vaccine Uptake ◽  
Cross Sectional ◽  
Health Concerns ◽  
Face To Face ◽  
Related Risk ◽  
Different Types

The present research examined which motivational factors contribute to individuals’ intention to take a vaccine that protects against SARS-CoV-2-virus and their self-reported vaccine uptake several months later. The role of different types of motivation was investigated (i.e., autonomous and controlled regulation) as well as vaccine distrust and effort to obtain a vaccine. Across two large-scale cross-sectional (N = 8887) and longitudinal (N = 6996) studies and controlling for various covariates, autonomous motivation and distrust-based amotivation contributed positively and negatively, respectively, to a) concurrent vaccination intentions, b) self-reported vaccination and c) subsequent subscription to a waitlist to obtain a vaccine. Participants’ infection-related risk perception predicted more positive vaccination outcomes through fostering greater autonomous motivation for vaccination and lower distrust, whereas pandemic-related health concerns failed to yield such adaptive effects. The results emphasize the importance of fostering autonomous motivation for vaccination and handling distrust, both at the societal and face-to-face level.

Sign in / Sign up

Export Citation Format

Share Document