scholarly journals The Lancaster Sensorimotor Norms: multidimensional measures of perceptual and action strength for 40,000 English words

2019 ◽  
Vol 52 (3) ◽  
pp. 1271-1291 ◽  
Author(s):  
Dermot Lynott ◽  
Louise Connell ◽  
Marc Brysbaert ◽  
James Brand ◽  
James Carney
Keyword(s):  
Web Application ◽  
Open Science ◽  
Grounded Cognition ◽  
Word Meanings ◽  
Link Type ◽  
Semantic Norms ◽  
Perceptual Modalities ◽  
Sensorimotor Information ◽  
Science Framework ◽  
Amazon's Mechanical Turk

AbstractSensorimotor information plays a fundamental role in cognition. However, the existing materials that measure the sensorimotor basis of word meanings and concepts have been restricted in terms of their sample size and breadth of sensorimotor experience. Here we present norms of sensorimotor strength for 39,707 concepts across six perceptual modalities (touch, hearing, smell, taste, vision, and interoception) and five action effectors (mouth/throat, hand/arm, foot/leg, head excluding mouth/throat, and torso), gathered from a total of 3,500 individual participants using Amazon’s Mechanical Turk platform. The Lancaster Sensorimotor Norms are unique and innovative in a number of respects: They represent the largest-ever set of semantic norms for English, at 40,000 words × 11 dimensions (plus several informative cross-dimensional variables), they extend perceptual strength norming to the new modality of interoception, and they include the first norming of action strength across separate bodily effectors. In the first study, we describe the data collection procedures, provide summary descriptives of the dataset, and interpret the relations observed between sensorimotor dimensions. We then report two further studies, in which we (1) extracted an optimal single-variable composite of the 11-dimension sensorimotor profile (Minkowski 3 strength) and (2) demonstrated the utility of both perceptual and action strength in facilitating lexical decision times and accuracy in two separate datasets. These norms provide a valuable resource to researchers in diverse areas, including psycholinguistics, grounded cognition, cognitive semantics, knowledge representation, machine learning, and big-data approaches to the analysis of language and conceptual representations. The data are accessible via the Open Science Framework (http://osf.io/7emr6/) and an interactive web application (https://www.lancaster.ac.uk/psychology/lsnorms/).

scholarly journals The Lancaster Sensorimotor Norms: Multidimensional measures of Perceptual and Action Strength for 40,000 English words

2019 ◽  
Author(s):  
Dermot Lynott ◽  
Louise Connell ◽  
Marc Brysbaert ◽  
James Brand ◽  
James Carney
Keyword(s):  
Web Application ◽  
Open Science ◽  
Grounded Cognition ◽  
Word Meanings ◽  
Semantic Norms ◽  
Perceptual Modalities ◽  
Sensorimotor Information ◽  
Science Framework ◽  
Amazon's Mechanical Turk ◽  
Decision Times

Sensorimotor information plays a fundamental role in cognition. However, existing materials that measure the sensorimotor basis to word meanings and concepts have been restricted in sample size and breadth of sensorimotor experience. Here, we present norms of sensorimotor strength for 39,707 concepts across six perceptual modalities (touch, hearing, smell, taste, vision, and interoception) and five action effectors (mouth/throat, hand/arm, foot/leg, head excluding mouth/throat, and torso), gathered from a total of 3,500 individual participants using Amazon's Mechanical Turk platform. The Lancaster Sensorimotor Norms are unique and innovative in a number of respects: they represent the largest ever set of semantic norms for English at 40 thousand words x 11 dimensions (plus several informative cross-dimensional variables); they extend perceptual strength norming to the new modality of interoception; and they include the first norming of action strength across separate bodily effectors. In the first study, we describe the data collection procedures, provide summary descriptives of the dataset, and interpret the relations observed between sensorimotor dimensions. We then report two further studies that i) extract an optimal single-variable composite of the 11-dimension sensorimotor profile (Minkowski 3 strength), and ii) demonstrate the utility of both perceptual and action strength in facilitating lexical decision times and accuracy in two separate datasets. These norms provide a valuable resource to researchers in diverse areas including psycholinguistics, grounded cognition, cognitive semantics, knowledge representation, machine learning, and big data approaches to the analysis of language and conceptual representations. The data are accessible via the Open Science Framework (http://osf.io/7emr6/ ) and an interactive web application (https://www.lancaster.ac.uk/psychology/lsnorms/).

scholarly journals Open Science Framework (OSF)

2017 ◽  
Vol 105 (2) ◽  
Author(s):  
Erin D. Foster, MSLS ◽  
Ariel Deardorff, MLIS
Keyword(s):  
Open Source ◽  
Web Application ◽  
Open Science ◽  
Science Framework ◽  
Free Open Source

The Open Science Framework (OSF) is a free, open source, research workflow web application developed and maintained by the Center for Open Science (COS).

scholarly journals Restoring invisible and abandoned trials of gabapentin for neuropathic pain: a clinical and methodological investigation

BMJ Open ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. e047785
Author(s):  
Evan Mayo-Wilson ◽  
Xiwei Chen ◽  
Riaz Qureshi ◽  
Stephanie Dickinson ◽  
Lilian Golzarri-Arroyo ◽  
...  
Keyword(s):  
Neuropathic Pain ◽  
Secondary Data ◽  
Open Science ◽  
Journal Articles ◽  
Link Type ◽  
Institutional Review ◽  
Individual Trial ◽  
Individual Participant ◽  
Review Protocol ◽  
Science Framework

IntroductionGabapentin (Neurontin) is prescribed widely for conditions for which it has not been approved by regulators, including certain neuropathic pain conditions. There is limited evidence that gabapentin is safe and effective for the treatment of neuropathic pain. Published trial reports, and systematic reviews based on published trial reports, mislead patients and providers because information about gabapentin’s harms has been published only partly. We confirmed that trials conducted by the drug developer have been abandoned, and we plan to conduct a restoration with support from the Restoring Invisible and Abandoned Trials Support Centre (https://restoringtrials.org/).Methods and analysisIn this study, we will analyse and report the harms that were observed in six trials of gabapentin, which have not been reported publicly (eg, in journal articles). We will use clinical study reports and individual participant data to identify and report the harms observed in each individual trial and to summarise the harms observed across all six trials. We will report all adverse events observed in the included trials by sharing deidentified data and summary tables on the Open Science Framework (https://osf.io/w8puv/). Additionally, we will produce a summary report that describes differences between the randomised groups in each trial and across trials for prespecified harms outcomes.Ethics and disseminationWe will use secondary data. This study was determined to be exempt from Institutional Review Board (IRB) review (protocol #1910607198).

scholarly journals Dutch sensory modality norms

2021 ◽  
Author(s):  
Laura J. Speed ◽  
Marc Brybaert
Keyword(s):  
Word Processing ◽  
Sensory Modality ◽  
Open Science ◽  
Large Sets ◽  
Strongly Connected ◽  
Perceptual Modalities ◽  
Word Classes ◽  
The Senses ◽  
Science Framework ◽  
The Relationship

AbstractMany words are strongly connected to the senses, such as vision, taste, and touch. In order to facilitate research on language and the senses, large sets of linguistic stimuli and their corresponding measures of sensory associations should be available. To aid in such investigations, we present a new set of sensory modality norms for over 24,000 Dutch words. The sensory norms comprise perceptual strength ratings in six perceptual modalities: audition, gustation, haptics, olfaction, vision, and interoception. The new norms improve on existing Dutch sensory norms in three ways: 1) they significantly expand on the number of words rated; 2) they include multiple word classes; 3) they add a new perceptual modality: interoception. We show that the sensory norms are able to predict word processing behavior and outperform existing ratings of sensory experience: concreteness and imageability. The data are available via the Open Science Framework (https://osf.io/ubvy2) and serve as a valuable resource for research into the relationship between language and perception.

scholarly journals Does pre-notification increase questionnaire response rates: a randomised controlled trial nested within a systematic review

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Benjamin Woolf ◽  
Phil Edwards
Keyword(s):  
Systematic Review ◽  
Controlled Trial ◽  
Response Rates ◽  
Open Science ◽  
Outcome Data ◽  
Absolute Difference ◽  
Questionnaire Response ◽  
Link Type ◽  
Science Framework ◽  
Randomised Controlled

Abstract Background Missing outcome data can lead to bias in the results of systematic reviews. One way to address missing outcome data is by requesting the data from the trial authors, but non-response is common. One way to potentially improve response rates is by sending study participants advance communication. During the update of a systematic review examining the effect of pre-notification on response rates, study authors needed to be contacted for further information. This study was nested within the systematic review by randomising authors to receive a notification of the upcoming request for information. The objective was to test if pre-notification increased response rates. Methods The participants were study authors included in the systematic review, whose studies were at unclear risk of bias. The intervention was a pre-notification of the request for further information, sent 1 day before the request. The outcome was defined as the proportion of authors who responded to the request for information. Authors were randomised by simple randomisation. Thirty three authors were randomised to the pre-notification arm, and 42 were randomised to the control arm. Authors were blinded to the possibility of an alternative condition. Results All authors randomised were analysed. 14/33 (42.4%) authors in the pre-notification arm had returned responses to the questionnaire, and 18/42 (42.9%) in the control arm. There was no evidence of a difference between these groups (absolute difference = − 0.5, 95% CI (− 23.4 to 22.5%), p = 1). We received no complaints about receiving the pre-notification. Conclusions This study’s results do not support the hypothesis that pre-notification increases response from study authors being contacted for a request for more information. However, the study has a low power, and the results may not generalise to other contexts, methods of administering a pre-notification, or study populations. Trial registration Registration and protocol: This trial is not registered with any trial registry. However, the protocol was posted in advance on the Open Science Framework website and is available on the Open Science Framework website: DOI: 10.17605/OSF.IO/MSV2W or https://osf.io/msv2w/

scholarly journals lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Fayaz Seifuddin ◽  
Komudi Singh ◽  
Abhilash Suresh ◽  
Jennifer T. Judy ◽  
Yun-Ching Chen ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Tissue Specificity ◽  
Expression Patterns ◽  
Open Science ◽  
Whole Genome Sequence ◽  
Tissue Specific ◽  
Normal Tissues ◽  
Link Type ◽  
Science Framework ◽  
User Friendly

Abstract Long non-coding RNA Knowledgebase (lncRNAKB) is an integrated resource for exploring lncRNA biology in the context of tissue-specificity and disease association. A systematic integration of annotations from six independent databases resulted in 77,199 human lncRNA (224,286 transcripts). The user-friendly knowledgebase covers a comprehensive breadth and depth of lncRNA annotation. lncRNAKB is a compendium of expression patterns, derived from analysis of RNA-seq data in thousands of samples across 31 solid human normal tissues (GTEx). Thousands of co-expression modules identified via network analysis and pathway enrichment to delineate lncRNA function are also accessible. Millions of expression quantitative trait loci (cis-eQTL) computed using whole genome sequence genotype data (GTEx) can be downloaded at lncRNAKB that also includes tissue-specificity, phylogenetic conservation and coding potential scores. Tissue-specific lncRNA-trait associations encompassing 323 GWAS (UK Biobank) are also provided. LncRNAKB is accessible at http://www.lncrnakb.org/, and the data are freely available through Open Science Framework (10.17605/OSF.IO/RU4D2).

scholarly journals Dutch Sensory Modality Norms

2020 ◽  
Author(s):  
Laura Jane Speed ◽  
Marc Brysbaert
Keyword(s):  
Word Processing ◽  
Sensory Modality ◽  
Word Meaning ◽  
Open Science ◽  
Perceptual Modality ◽  
Sensory Modalities ◽  
Perceptual Modalities ◽  
Word Classes ◽  
Science Framework ◽  
The Relationship

Word meaning is thought to be grounded in the sensory modalities. In order to test such hypotheses in experiments, linguistic stimuli needs to be carefully selected and controlled for. To aid in such investigations, we present a new set of sensory modality norms for over 24,000 Dutch words. The sensory norms comprise perceptual strength ratings in six perceptual modalities: audition, gustation, haptics, olfaction, vision, and interoception. The new norms improve on existing Dutch sensory norms in three ways: 1) they significantly expand on the number of words rated; 2) they include multiple word classes; 3) they add a new perceptual modality: interoception. We show that the sensory norms are able to predict word processing behavior and outperform existing ratings of sensory experience: concreteness and imageability. The data are available via the Open Science Framework (https://osf.io/ubvy2) and serve as a valuable resource for research into the relationship between language and perception.

Publikasi Akademik Sepanjang 2019

2019 ◽  
Author(s):  
Adib Rifqi Setiawan
Keyword(s):  
Open Science ◽  
Research Papers ◽  
Science Framework

Berikut ini beberapa publikasi saya pada 2019 ini. Penting atau tidak, saya menganggap bahwa publikasi hanyalah efek samping riset. Di luar publikasi ini, saya juga masih aktif sebagai penulis media daring, seperti Qureta.com, Selasar.com, dan SantriMilenial.net serta mengunggah beberapa artikel preprint melalui layanan Open Science Framework (OSF), EdArxiv.org, dan Research Papers in Economics (RePEc).

scholarly journals AB0210 ACREULAR: AN R PACKAGE FOR THE CALCULATION AND VISUALISATION OF ACR/EULAR RELATED RHEUMATOID ARTHRITIS MEASURES

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1405.1-1406
Author(s):  
F. Morton ◽  
J. Nijjar ◽  
C. Goodyear ◽  
D. Porter
Keyword(s):  
Rheumatoid Arthritis ◽  
Functional Status ◽  
Rheumatic Diseases ◽  
Web Application ◽  
R Package ◽  
Diagnostic Classification ◽  
Microsoft Excel ◽  
Link Type ◽  
Large Joint ◽  
Programming Skills

Background:The American College of Rheumatology (ACR) and the European League Against Rheumatism (EULAR) individually and collaboratively have produced/recommended diagnostic classification, response and functional status criteria for a range of different rheumatic diseases. While there are a number of different resources available for performing these calculations individually, currently there are no tools available that we are aware of to easily calculate these values for whole patient cohorts.Objectives:To develop a new software tool, which will enable both data analysts and also researchers and clinicians without programming skills to calculate ACR/EULAR related measures for a number of different rheumatic diseases.Methods:Criteria that had been developed by ACR and/or EULAR that had been approved for the diagnostic classification, measurement of treatment response and functional status in patients with rheumatoid arthritis were identified. Methods were created using the R programming language to allow the calculation of these criteria, which were incorporated into an R package. Additionally, an R/Shiny web application was developed to enable the calculations to be performed via a web browser using data presented as CSV or Microsoft Excel files.Results:acreular is a freely available, open source R package (downloadable fromhttps://github.com/fragla/acreular) that facilitates the calculation of ACR/EULAR related RA measures for whole patient cohorts. Measures, such as the ACR/EULAR (2010) RA classification criteria, can be determined using precalculated values for each component (small/large joint counts, duration in days, normal/abnormal acute-phase reactants, negative/low/high serology classification) or by providing “raw” data (small/large joint counts, onset/assessment dates, ESR/CRP and CCP/RF laboratory values). Other measures, including EULAR response and ACR20/50/70 response, can also be calculated by providing the required information. The accompanying web application is included as part of the R package but is also externally hosted athttps://fragla.shinyapps.io/shiny-acreular. This enables researchers and clinicians without any programming skills to easily calculate these measures by uploading either a Microsoft Excel or CSV file containing their data. Furthermore, the web application allows the incorporation of additional study covariates, enabling the automatic calculation of multigroup comparative statistics and the visualisation of the data through a number of different plots, both of which can be downloaded.Figure 1.The Data tab following the upload of data. Criteria are calculated by the selecting the appropriate checkbox.Figure 2.A density plot of DAS28 scores grouped by ACR/EULAR 2010 RA classification. Statistical analysis has been performed and shows a significant difference in DAS28 score between the two groups.Conclusion:The acreular R package facilitates the easy calculation of ACR/EULAR RA related disease measures for whole patient cohorts. Calculations can be performed either from within R or by using the accompanying web application, which also enables the graphical visualisation of data and the calculation of comparative statistics. We plan to further develop the package by adding additional RA related criteria and by adding ACR/EULAR related measures for other rheumatic disorders.Disclosure of Interests:Fraser Morton: None declared, Jagtar Nijjar Shareholder of: GlaxoSmithKline plc, Consultant of: Janssen Pharmaceuticals UK, Employee of: GlaxoSmithKline plc, Paid instructor for: Janssen Pharmaceuticals UK, Speakers bureau: Janssen Pharmaceuticals UK, AbbVie, Carl Goodyear: None declared, Duncan Porter: None declared

scholarly journals Genetic and Transcriptomic Biomarkers in Neurodegenerative Diseases: Current Situation and the Road Ahead

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1030
Author(s):  
Julie Lake ◽  
Catherine S. Storm ◽  
Mary B. Makarious ◽  
Sara Bandres-Ciga
Keyword(s):  
Neurodegenerative Diseases ◽  
Large Scale ◽  
Disease Diagnosis ◽  
Open Science ◽  
Future Directions ◽  
The Road ◽  
Current State ◽  
Molecular Complexity ◽  
Science Framework ◽  
Lateral Sclerosis

Neurodegenerative diseases are etiologically and clinically heterogeneous conditions, often reflecting a spectrum of disease rather than well-defined disorders. The underlying molecular complexity of these diseases has made the discovery and validation of useful biomarkers challenging. The search of characteristic genetic and transcriptomic indicators for preclinical disease diagnosis, prognosis, or subtyping is an area of ongoing effort and interest. The next generation of biomarker studies holds promise by implementing meaningful longitudinal and multi-modal approaches in large scale biobank and healthcare system scale datasets. This work will only be possible in an open science framework. This review summarizes the current state of genetic and transcriptomic biomarkers in Parkinson’s disease, Alzheimer’s disease, and amyotrophic lateral sclerosis, providing a comprehensive landscape of recent literature and future directions.

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