scholarly journals Creating clear and informative image-based figures for scientific publications

PLoS Biology ◽  
2021 ◽  
Vol 19 (3) ◽  
pp. e3001161
Author(s):  
Helena Jambor ◽  
Alberto Antonietti ◽  
Bradly Alicea ◽  
Tracy L. Audisio ◽  
Susann Auer ◽  
...  
Keyword(s):  
Cell Biology ◽  
Image Acquisition ◽  
Good Practice ◽  
Quality Standards ◽  
Image Manipulation ◽  
Scientific Publications ◽  
Image Magnification ◽  
Plant Sciences ◽  
Technical Specifications ◽  
Common Problems

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in 3 fields; plant sciences, cell biology, and physiology (n = 580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

scholarly journals Creating Clear and Informative Image-based Figures for Scientific Publications

2020 ◽  
Author(s):  
Helena Jambor ◽  
Alberto Antonietti ◽  
Bradly Alicea ◽  
Tracy L. Audisio ◽  
Susann Auer ◽  
...  
Keyword(s):  
Cell Biology ◽  
Image Acquisition ◽  
Good Practice ◽  
Quality Standards ◽  
Image Manipulation ◽  
Scientific Publications ◽  
Image Magnification ◽  
Plant Sciences ◽  
Technical Specifications ◽  
Common Problems

AbstractScientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in three fields; plant sciences, cell biology and physiology. Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

scholarly journals Flow cytometry as tool in plant sciences, with emphasis on genome size and ploidy level assessment

2018 ◽  
Vol 2 (2) ◽  
pp. 1 ◽  
Author(s):  
Mickael Bourge ◽  
Spencer Creig Brown ◽  
Sonja Siljak-Yakovlev
Keyword(s):  
Flow Cytometry ◽  
Genome Size ◽  
Ploidy Level ◽  
Cell Biology ◽  
Base Composition ◽  
Good Practice ◽  
Plant Cells ◽  
Size Measurement ◽  
Fast Acquisition ◽  
Plant Sciences

Flow cytometry has become the method of choice to measure the DNA content (genome size) in plants. Ease of sample preparation, fast acquisition, and accurate measurements have made the method popular in the domains of plant cell biology, systematics, evolution, genetics and biotechnology. Although the cell wall is a problem when isolating plant cells, cytometry remains a powerful tool in plant sciences. Based on our 30-years’ experience in this field, this review will focus at first on genome size measurement using simply isolated nuclei: the good practice for acquisition, nuclei isolation, appropriate buffers, kind of tissues to use. The second part will briefly review what kind of measurements it is possible to make in plant cytometry, and for what purpose: base composition, ploidy level, cell cycle, endoreplication, seed screening, and nuclei/chromosomes sorting. We will address troubleshooting. The commonly-used mathematic tools will be discussed.

How is science to be carried forward, and its conclusions reported?

2018 ◽  
Author(s):  
Andrew Briggs ◽  
Hans Halvorson ◽  
Andrew Steane
Keyword(s):  
Mathematical Proof ◽  
Good Practice ◽  
Natural World ◽  
Component Part ◽  
Journal Articles ◽  
Scientific Publications ◽  
Direct Role ◽  
Intellectual Activity ◽  
Self Identity ◽  
The World

The chapter appraises science as an intellectual activity that is appropriately carried out on its own terms. Consequently, it is not appropriate to introduce references to God as a component part of a mathematical proof, nor of a system of forces in the natural world, nor of a sequence of impersonal processes in the biosphere. This does not mean that it is inappropriate to be thankful to God and to celebrate all these aspects of the world as gifts. They can be employed as opportunities to express appreciation through studying and understanding them better in their own right. Nevertheless, there may be processes, such as those which shape a person’s self-identity, in which it is appropriate to recognize God’s more direct role. Good practice concerning acknowledgements sections in scientific publications such as doctoral theses and journal articles is then discussed.

scholarly journals Mask R-CNN Based C. Elegans Detection with a DIY Microscope

Biosensors ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 257
Author(s):  
Sebastian Fudickar ◽  
Eike Jannik Nustede ◽  
Eike Dreyer ◽  
Julia Bornhorst
Keyword(s):  
Cell Biology ◽  
High Throughput Screening ◽  
Low Cost ◽  
Image Acquisition ◽  
Rapid Development ◽  
Model Organism ◽  
Large Data ◽  
Data Set ◽  
C Elegans ◽  
Do It Yourself

Caenorhabditis elegans (C. elegans) is an important model organism for studying molecular genetics, developmental biology, neuroscience, and cell biology. Advantages of the model organism include its rapid development and aging, easy cultivation, and genetic tractability. C. elegans has been proven to be a well-suited model to study toxicity with identified toxic compounds closely matching those observed in mammals. For phenotypic screening, especially the worm number and the locomotion are of central importance. Traditional methods such as human counting or analyzing high-resolution microscope images are time-consuming and rather low throughput. The article explores the feasibility of low-cost, low-resolution do-it-yourself microscopes for image acquisition and automated evaluation by deep learning methods to reduce cost and allow high-throughput screening strategies. An image acquisition system is proposed within these constraints and used to create a large data-set of whole Petri dishes containing C. elegans. By utilizing the object detection framework Mask R-CNN, the nematodes are located, classified, and their contours predicted. The system has a precision of 0.96 and a recall of 0.956, resulting in an F1-Score of 0.958. Considering only correctly located C. elegans with an [email protected] IoU, the system achieved an average precision of 0.902 and a corresponding F1 Score of 0.906.

scholarly journals British Thoracic Society Quality Standards for outpatient management of pulmonary embolism

2020 ◽  
Vol 7 (1) ◽  
pp. e000636
Author(s):  
Robin Condliffe ◽  
Paul Albert ◽  
Raza Alikhan ◽  
Emma Gee ◽  
Daniel Horner ◽  
...  
Keyword(s):  
Pulmonary Embolism ◽  
Service Providers ◽  
Good Practice ◽  
Quality Standards ◽  
Quality Standard ◽  
Standards Of Care ◽  
British Thoracic Society ◽  
Dissemination And Implementation ◽  
Outpatient Management ◽  
The Uk

IntroductionThe purpose of the quality standards document is to provide healthcare professionals, commissioners, service providers and patients with a guide to standards of care that should be met for outpatient management of pulmonary embolism in the UK, together with measurable markers of good practice. Quality statements are based on the British Thoracic Society (BTS) Guideline for the Initial Outpatient Management of Pulmonary Embolism.MethodsDevelopment of BTS Quality Standards follows the BTS process of quality standard production based on the National Institute for Health and Care Excellence process manual for the development of quality standards.ResultsSix quality statements have been developed, each describing a standard of care for the outpatient management of pulmonary embolism in the UK, together with measurable markers of good practice.DiscussionBTS Quality Standards for Outpatient Management of Pulmonary Embolism form a key part of the range of supporting materials that the society produces to assist in the dissemination and implementation of a guideline’s recommendations.

Technology transfer

1989 ◽  
Vol 3 (1) ◽  
pp. 27-32 ◽  
Author(s):  
Allan D. Barnes
Keyword(s):  
Technology Transfer ◽  
Good Practice ◽  
General Lack ◽  
European Universities ◽  
Develop Technology ◽  
Common Problems ◽  
The Uk ◽  
Media Channel

Four technology transfer practitioners from the UK set out to examine the technology transfer activities of four European universities, looking for examples of good practice, innovative schemes and common problems. This article gives a summary of their report. The conclusions drawn are that universities in general lack clear plans to develop technology transfer activities, that there is little sharing of experiences between universities, and that there is not an appropriate media channel for the technology transfer industry. The author forwards recommendations in view of these conclusions.

scholarly journals SOCIAL ENTREPRENEURSHIP AND EMPLOYMENT CHALLENGES OF PERSONS WITH MENTAL DISABILITIES

2020 ◽  
Author(s):  
Evija Anca ◽  
Biruta Sloka
Keyword(s):  
Public Policy ◽  
Research Methods ◽  
Social Entrepreneurship ◽  
Statistical Data ◽  
Good Practice ◽  
Academic Research ◽  
Developed Countries ◽  
Mental Disabilities ◽  
Scientific Publications ◽  
Development Scenarios

In developed countries there is a valuable experience how to include people with disabilities into society: involve in several activities and let them know as people valuable for the society. More and more academic research is devoted to those aspects as well as public policy is developed to create and support social entrepreneurship. Aim of the paper is to analyse findings and good practice of employment of people with mental disabilities in several countries and analyse the situation and possible developments on employment of people with mental disabilities in Latvia. Tasks of research: 1) analyse results of academic findings on good practice and challenges in employment of people with mental disabilities wold-wide; 2) analyse the developments and trends on employment of people with mental disabilities in Latvia; 3) propose possible development scenarios on employment of people with mental disabilities in Latvia. Research methods used in research: scientific publications analysis; analysis of legislative documents on employment of people with mental disabilities, analysis of statistical data on employment of people with mental disabilities. Research results have shown that in recent years many important steps in employment of people with mental disabilities in Latvia has been reached but there are some difficulties in realise of sustainability in this aspect.

scholarly journals IdRef, Paprika and Qualinka. A toolbox for authority data quality and interoperability

ABI-Technik ◽  
2020 ◽  
Vol 40 (2) ◽  
pp. 158-168
Author(s):  
Aline Le Provost ◽  
Yann Nicolas
Keyword(s):  
Data Quality ◽  
Reference Data ◽  
Open Data ◽  
Quality Standards ◽  
High Quality ◽  
Scientific Publications ◽  
The Core

AbstractAuthority data has always been at the core of library catalogues. Today, authority data is reference data on a wider scale. The former authorities of the “Sudoc” union catalogue mutated into “IdRef”, a read/write platform of open data and services which seeks to become a national supplier of reliable identifiers for French universities. To support their dissemination and comply with high quality standards, Paprika and Qualinka have been added to our toolbox, to expedite the massive and secure linking of scientific publications to IdRef authorities.

scholarly journals TINJAUAN TERHADAP PLTS 24 KW ATAP GEDUNG PT INDONESIA POWER PESANGGARAN BALI

2018 ◽  
Vol 5 (2) ◽  
pp. 26
Author(s):  
Ketut Vidhia Kumara ◽  
I Nyoman Satya Kumara ◽  
Wayan Gede Ariastina
Keyword(s):  
Energy Production ◽  
Good Practice ◽  
Slope Angle ◽  
International Standards ◽  
Solar Pv ◽  
Solar Module ◽  
Technical Data ◽  
Optimum Energy ◽  
Technical Specifications ◽  
The Cost

PT. Indonesia Power unit Pesanggaran is one of the power generation companies in Bali, which has also participated in the development of renewable energy by installing solar PV with a capacity of 24 KW. In this research, reviews was conducted to know the condition of the solar PV plant. Review is carried out by conducting observation in the field, reviewing technical data of solar PV components, and also interviews with the staff who operate and maintain the solar PV. Through reviews it was found that the design and installation of solar PV plant is good and follows good practice of solar PV installation for optimum energy production. Due to plant location at GPS coordinate of -8,72, 115,21 therefore the solar module has been installed facing north or azimuth 0o. This module is placed on the roof of Building A, thereby reducing the cost to construct mechanical supports. The solar module was installed with a slope angle of 22o approaching the optimum slope angle. The components of the PV plant are good as they bear international standards. The solar module is CHN240-60P polycrystalline silicon with 60 cells that caccries CE certificate (Conformité Europeenne). Also, the inverter is three units of ABB PVS300-TL-800W-2 with AC output of 8,000 W which are also carries CE certificate and others. The quality of technical specifications of solar PV components and also installation of the plant has direct influence on the energy production of the plant and these have been properly implemented on the 24 KW Indonesia Power solar PV plant.

scholarly journals Development of methodological guidance, publication standards and training materials for realist and meta-narrative reviews: the RAMESES (Realist And Meta-narrative Evidence Syntheses – Evolving Standards) project

2014 ◽  
Vol 2 (30) ◽  
pp. 1-252 ◽  
Author(s):  
Geoff Wong ◽  
Trish Greenhalgh ◽  
Gill Westhorp ◽  
Ray Pawson
Keyword(s):  
Evidence Synthesis ◽  
Good Practice ◽  
Quality Standards ◽  
Mailing List ◽  
Delphi Panel ◽  
Secondary Research ◽  
Training Materials ◽  
Time Problem ◽  
And Training ◽  
Publication Standards

BackgroundThere is growing interest in theory-driven, qualitative and mixed-method approaches to systematic review, such as realist and meta-narrative review. These approaches offer the potential to expand the knowledge base in policy-relevant areas. However, the quality of such reviews can be difficult to assess.ObjectivesThe aim of this project was to produce methodological guidance, publication standards and training resources for those seeking to undertake realist and/or meta-narrative reviews.Methods/designWe (1) collated and summarised existing literature on the principles of good practice in realist and meta-narrative systematic reviews; (2) considered the extent to which these principles had been followed by published and in-progress reviews, thereby identifying how rigour may have been lost and how existing methods could be improved; (3) used an online Delphi method with an interdisciplinary panel of experts from academia and policy, to produce a draft set of methodological steps and publication standards; (4) produced training materials with learning objectives linked to these steps; (5) refined these standards and training materials prospectively on real reviews in progress, capturing methodological and other challenges as they arose; (6) synthesised expert input, evidence review and real-time problem analysis into more definitive guidance and standards; and (7) disseminated outputs to audiences in academia and policy.ResultsAn important element of this study was the establishment of an e-mail mailing list to bring together researches in the field (www.jiscmail.ac.uk/RAMESES). Our literature review identified 35 and nine realist and meta-narrative reviews respectively. Analysis and discussion within the project team produced a summary of the published literature, and common questions and challenges into briefing materials for the Delphi panel, comprising 37 and 33 members (for realist and meta-narrative reviews respectively). Within three rounds this panel had reached a consensus on 19 (realist) and 20 (meta-narrative) key publication standards, with an overall response rate of 90% and 91% respectively. The Realist And Meta-narrative Evidence Syntheses – Evolving Standards (RAMESES) publication standards for realist syntheses and meta-narrative reviews were published in open-access journals and quickly became highly accessed. The RAMESES quality standards and training materials drew together the following sources of data: (1) personal expertise as researchers and trainers; (2) data from the Delphi panels; (3) feedback from participants at training sessions we ran; and (4) comments made on RAMESES mailing list. The quality standards and training materials are freely available online (www.ramesesproject.org).DiscussionThe production of these standards and guidance drew on multiple sources of knowledge and expertise, and a high degree of a consensus was achieved despite ongoing debate among researchers about the overall place of these methodologies in the secondary research toolkit. As with all secondary research methods, guidance on quality assurance and uniform reporting is an important step towards improving quality and consistency of studies. We anticipate that as more reviews are undertaken, further refinement will be needed to the publication and quality standards and training materials.LimitationsThe project’s outputs are not definitive and in the future updating and further development is likely to be needed.ConclusionAn initial set of publication standards, quality standards and training materials have been produced for researchers, users and funders of realist or meta-narrative reviews. As realist and meta-narrative reviews are relatively new approaches to evidence synthesis, methodological development is needed for both review approaches.FundingThe National Institute for Health Research Health Services and Delivery Research programme.

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