scholarly journals Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects

Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 750 ◽  
Author(s):  
Pia Anneli Sofia Kinaret ◽  
Angela Serra ◽  
Antonio Federico ◽  
Pekka Kohonen ◽  
Penny Nymark ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Experimental Design ◽  
Chemical Compounds ◽  
Alternative Methods ◽  
Data Generation ◽  
Rna Seq ◽  
Chemical Toxicity ◽  
Environmental Chemical ◽  
Regulatory Aspects ◽  
Starting Point

The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms’ responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.

scholarly journals The Violence of the Cut: Gendering Self-Harm

2021 ◽  
Vol 18 (9) ◽  
pp. 4650
Author(s):  
Amy Chandler ◽  
Zoi Simopoulou
Keyword(s):  
Pilot Study ◽  
Data Generation ◽  
Male And Female ◽  
Female Violence ◽  
Starting Point ◽  
Self Harm ◽  
Qualitative Methodologies ◽  
Qualitative Exploration

Taking as a starting point the frequent characterisation of self-harm as “an adolescent thing for girls,” this paper offers a sociologically informed, qualitative exploration of self-harm as a gendered practice. We move beyond statistical constructions of this “reality,” and critically examine how this characterisation comes to be, and some of its effects. Our data are drawn from a pilot study that developed a collaborative arts-based inquiry into meanings of self-harm. The authors worked with two groups: one of practitioners and another of people who had self-harmed, meeting over six sessions to discuss and make art in response to a range of themes relating to the interpretation and explanation of self-harm. Through data generation and analysis, we collaboratively seek to make sense of the gendering of self-harm, focusing on a series of dualistic Cartesian “cuts” between male and female, violence and vulnerability, and inside and outside. In conclusion, we call for more multi- and interdisciplinary explorations of self-harm, and greater use of diverse, arts-based, and qualitative methodologies, in order to further expand and nuance understandings and ethical engagements with self-harm, and those who are affected by it.

scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

scholarly journals Chemical monitoring of Swedish coastal waters indicates common exceedances of environmental thresholds, both for individual substances as well as their mixtures

2017 ◽  
Author(s):  
Mikael B Gustavsson ◽  
Jörgen Magnér ◽  
Bethanie Carney Almroth ◽  
Martin K Eriksson ◽  
Joachim Sturve ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Concentration Addition ◽  
Chemical Pollution ◽  
Chemical Contamination ◽  
Total Risk ◽  
Environmental Chemical ◽  
Swedish West Coast ◽  
Chemical Monitoring ◽  
Chemical Risk Assessment ◽  
The Individual

Chemical pollution was monitored and assessed along the Swedish west coast. 62 of 172 analyzed organic chemicals were detected in the water phase of at least one of five monitored sites. A Concentration Addition based screening-level risk assessment indicates that all sites are put at risk from chemical contamination, with total risk quotients between 2 and 9. Only at one site did none of the individual chemicals exceeded its individual environmental threshold (PNEC, EQS). The monitoring data thus demonstrate a widespread blanket of diffuse pollution, with no clear trends amongst sites. Further issues critical for the environmental chemical risk assessment include the challenges to achieve sufficiently low levels of detection especially for hormones and cybermethrin (a pyrethroid insecticide), the appropriate consideration of non-detects and the limited availability of reliable PNECs and EQS values.

scholarly journals Review of Chemical toxicity in Cosmetic products w.s.r. Dushi Visha

2019 ◽  
Vol 7 (07) ◽  
Author(s):  
Shubhangi Karanje
Keyword(s):  
Coal Tar ◽  
Chemical Compounds ◽  
The Body ◽  
The Self ◽  
Synthetic Method ◽  
Cosmetic Products ◽  
Chemical Toxicity ◽  
External Application ◽  
Self Confidence ◽  
Concept Of Beauty

 The concept of beauty and cosmetic is as old as mankind and civilization. Cosmetic product for females like sun scream, lipsticks, facial cream, nail paints, deodorants and sindoor are very popular in the market. They are generally the combination of various chemical compounds and some of them are derived from natural sources and others from synthetic method. In females regular external application of cosmetic products to improve beauty and appearance of a person which increases the self confidence. Most of the cosmetic products contains hazardous chemicals like talcum, parabens, coal, tar dye, phthalates, fragrance, tri ethanolamine and use of some heavy metals e.g. lead, mercury etc. Peoples are not aware of adverse effect of regular use of cosmetic products it accumulates in the body can cause contact dermatitis, skin disorders, allergies, hair loss and effect on nails etc. In Ayurveda cosmetic toxicity is compare to cumulative type of toxicity, so the cumulative type of toxicity is similar to Dushi Visha describes in Ayurveda.

Toward a More Nuanced Perception of Alzheimer’s Disease

2012 ◽  
Vol 27 (6) ◽  
pp. 388-396 ◽  
Author(s):  
Baldwin Van Gorp ◽  
Tom Vercruysse ◽  
Jan Van den Bulck
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Experimental Design ◽  
Fear Of Death ◽  
The Public ◽  
Starting Point

Starting point of this study was the assumption that Alzheimer’s disease is made worse for the person who has the disease by the negative regard in which the illness is held by society. The aim was to test by means of a campaign advertisement whether more nuanced counterframes could have an impact while remaining credible and comprehensible to the public. A sample of thousand people living in Belgium evaluated the campaign in an experimental design. This revealed that all the versions tested achieved a high average evaluation. The ad in which the heading referred to the fear of death and degeneration was judged to be most attention-grabbing, easier to understand, and more credible than the alternative heading with the idea that someone with Alzheimer’s could still enjoy playing cards. Together, these findings provided a basis for the use of counterframes to generating a more nuanced image of Alzheimer’s disease.

Business Modeling to Improve Auditor Risk Assessment: An Investigation of Alternative Representations

2014 ◽  
Vol 28 (2) ◽  
pp. 231-256 ◽  
Author(s):  
J. Efrim Boritz ◽  
Carla Carnaghan ◽  
Paulo S. Alencar
Keyword(s):  
Risk Assessment ◽  
Business Model ◽  
Business Models ◽  
Financial Statement ◽  
Alternative Methods ◽  
Audit Risk ◽  
Strategic Goals ◽  
Diagrammatic Representations ◽  
Model Components ◽  
The Relationship

ABSTRACT This study investigates the effects of alternative methods for documenting business models on audit risk assessment behavior. We consider tabular versus diagrammatic representations of the relationship between business model components such as environmental factors, strategic goals, internal processes and resources, and financial statement accounts. Multiple scenarios based on a real company were constructed and 24 participants, including audit partners, managers, and novice auditors performed a risk assessment for each scenario, presented in either a diagrammatic or a tabular format. The participants' verbal discussions as they performed the risk assessments were tape recorded, transcribed, and coded. A content analysis of the participants' coded verbal behavior indicates that the tabular presentation appears to elicit more frequent mention of accounts by the participants, while the diagram format leads to more mentions of other business model components. There is also some evidence of expertise effects. This study indicates that a tabular presentation can possess many of the benefits often associated with a diagrammatic representation. However, in our study, obtaining such benefits involved the deliberate structuring of the tabular presentation to organize the components of the business model and the links between them and financial statement accounts.

scholarly journals Intuitive Web-Based Experimental Design for High-Throughput Biomedical Data

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Andreas Friedrich ◽  
Erhan Kenar ◽  
Oliver Kohlbacher ◽  
Sven Nahnsen
Keyword(s):  
Big Data ◽  
Experimental Design ◽  
High Throughput ◽  
Large Scale ◽  
Integrated Design ◽  
Added Value ◽  
Biomedical Data ◽  
Data Generation ◽  
Web Based ◽  
Data Annotation

Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to keep track of the experimental design, including the conditions that are studied as well as information that might be interesting for failure analysis or further experiments in the future. In addition to the management of this information, means for an integrated design and interfaces for structured data annotation are urgently needed by researchers. Here, we propose a factor-based experimental design approach that enables scientists to easily create large-scale experiments with the help of a web-based system. We present a novel implementation of a web-based interface allowing the collection of arbitrary metadata. To exchange and edit information we provide a spreadsheet-based, humanly readable format. Subsequently, sample sheets with identifiers and metainformation for data generation facilities can be created. Data files created after measurement of the samples can be uploaded to a datastore, where they are automatically linked to the previously created experimental design model.

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