Browsing by Subject "RISK-ASSESSMENT"

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  • Browne, Thomas; Taylor, Rocky; Veitch, Brian; Helle, Inari; Parviainen, Tuuli; Khan, Faisal; Smith, Doug (2022)
    Risk aggregation is the process of combining multiple individual risks to develop a better understanding of the overall risk on a system. Different risks can have different consequences and different units of measure. This study contributes to the process of risk aggregation by presenting a general method to combine multiple consequences posed by an Arctic ship accident. The method considers ecological and socio-economic consequences of a potential oil spill, and life-safety consequences of a potential ship evacuation. Existing models for each consequence type are adopted. Individual consequence types are monetized and combined to quantify total consequence cost for a given accident scenario. A framework is proposed to assign a qualitative rating for total consequence severity. The qualitative scales of the framework are established using the quantitative method. Total consequence severity is evaluated for different ship types and regions in the Canadian Arctic. Results indicate that Arctic ship accidents involving oil tankers in environmentally sensitive regions and cruise ships in regions associated with long response times are worst-case scenarios, with similar total consequence severity levels. Implications for safe Arctic shipping are that on the basis of total consequence severity, mitigating the potential consequence severity of Arctic cruise operations is of near equal priority to that of Arctic tanker operations. Evaluating total consequence severity of potential Arctic ship accidents provides decision-makers and risk analysts with a data-driven tool to integrate multidisciplinary knowledge for the assessment, management, and communication of Arctic shipping risks.
  • Kohonen, Pekka; Parkkinen, Juuso A.; Willighagen, Egon L.; Ceder, Rebecca; Wennerberg, Krister; Kaski, Samuel; Grafstrom, Roland C. (2017)
    Predicting unanticipated harmful effects of chemicals and drug molecules is a difficult and costly task. Here we utilize a 'big data compacting and data fusion'-concept to capture diverse adverse outcomes on cellular and organismal levels. The approach generates from transcriptomics data set a 'predictive toxicogenomics space' (PTGS) tool composed of 1,331 genes distributed over 14 overlapping cytotoxicity-related gene space components. Involving similar to 2.5 x 10(8) data points and 1,300 compounds to construct and validate the PTGS, the tool serves to: explain dose-dependent cytotoxicity effects, provide a virtual cytotoxicity probability estimate intrinsic to omics data, predict chemically-induced pathological states in liver resulting from repeated dosing of rats, and furthermore, predict human drug-induced liver injury (DILI) from hepatocyte experiments. Analysing 68 DILI-annotated drugs, the PTGS tool outperforms and complements existing tests, leading to a hereto-unseen level of DILI prediction accuracy.
  • Saraceni, Francesco; Labopin, Myriam; Forcade, Edouard; Kroeger, Nicolaus; Socie, Gerard; Niittyvuopio, Riitta; Cornelissen, Jan J.; Labussiere-Wallet, Helene; Blaise, Didier; Choi, Goda; Byrne, Jenny L.; Guillerm, Gaelle; Marchand, Tony; Esteve, Jordi; Bazarbachi, Ali; Savani, Bipin; Olivieri, Attilio; Nagler, Arnon; Mohty, Mohamad (2021)
    Limited data are currently available on the outcome of patients with acute myeloid leukemia (AML) undergoing allogeneic stem cell transplantation (allo-SCT) with a reduced performance status. We herein present the results of a registry study on 2,936 AML patients undergoing allo-SCT in first remission (CR1) with a Karnofsky Performance Status (KPS) score less than or equal to 80%. Two-year leukemia-free survival (LFS), overall survival (OS) and graft-versus-host disease (GVHD)-free, and relapse-free survival (GRFS) rates were 54%, 59%, and 41%, respectively. In multivariable analysis, patients with a KPS score = 80% had lower non-relapse mortality (NRM) and superior OS in comparison to patients with a KPS score
  • Hagner, M.; Romantschuk, M.; Penttinen, O. -P.; Egfors, A.; Marchand, C.; Augustsson, A. (2018)
    The present study addresses toxicological properties of metal contaminated soils, using glassworks sites in south-easternl Sweden as study objects. Soil from five selected glassworks sites as well as from nearby reference areas were analysed for total and water-soluble metal concentrations and general geochemical parameters. A battery of biotests was then applied to assess the toxicity of the glassworks soil environments: a test of phytotoxicity with garden cress (Lepidium sativum); the BioTox(TM) test for toxicity to bacteria using Vibrio fischeri; and analyses of abundancies and biomass of nematodes and enchytraeids. The glassworks-and reference areas were comparable with respect to pH and the content of organic matter and nutrients (C, N, P), but total metal concentrations (Pb, As, Ba, Cd and Zn) were significantly higher at the former sites. Higher metal concentrations in the water-soluble fraction were also observed, even though these concentrations were low compared to the total ones. Nevertheless, toxicity of the glassworks soils was not detected by the two ex situ tests; inhibition of light emission by V. fischeri could not be seen, nor was an effect seen on the growth of L. sativum. A decrease in enchytraeid and nematode abundance and biomass was, however, observed for the landfill soils as compared to reference soils, implying in situ toxicity to soil-inhabiting organisms. The confirmation of in situ bioavailability and negative effects motivates additional studies of the risk posed to humans of the glassworks villages. (C) 2017 Published by Elsevier B.V.
  • Vuorinen, Pekka J.; Saulamo, Kari; Lecklin, Tiina; Rahikainen, Mika; Koivisto, Pertti; Keinänen, Marja (2017)
    Female perch (Perca fluviatilis) were sampled annually in late summer from 2006 to 2009 from the open sea of the eastern Gulf of Finland off Haapasaari island to monitor baseline biliary PAH metabolite concentrations. In addition, two coastal locations were sampled in 2008. PAH metabolite concentrations were compared between the open sea and coastal samples and between the sampling years and examined in relation to the body characteristics of perch. Of the PAH metabolites, only 1-hydroxypyrene (1 -OH pyrene) was detected at quantifiable levels in the bile of nearly all perch individuals. There were some annual differences but no temporal trend in the concentration of biliary 1-OH pyrene in perch from Haapasaari. At the coastal locations, 1-OH pyrene concentrations in the bile of perch were significantly higher than in the open sea Haapasaari area, probably due to greater contamination of the coastal sites and differences in feeding behaviour. No correlations between the body characteristics of perch and 1 -OH pyrene concentrations were detected. It is concluded that PAH metabolites in the bile of fish could be measured in the Gulf of Finland to detect oil spills in the open sea, and the cost-effective total fluorescence method could be used in such monitoring programmes. (C) 2017 Elsevier B.V. All rights reserved.
  • Brandao, Joao; Weiskerger, Chelsea; Valerio, Elisabete; Pitkänen, Tarja; Meriläinen, Päivi; Avolio, Lindsay; Heaney, Christopher D.; Sadowsky, Michael J. (2022)
    Beach sand and water have both shown relevance for human health and their microbiology have been the subjects of study for decades. Recently, the World Health Organization recommended that recreational beach sands be added to the matrices monitored for enterococci and Fungi. Global climate change is affecting beach microbial contamination, via changes to conditions like water temperature, sea level, precipitation, and waves. In addition, the world is changing, and humans travel and relocate, often carrying endemic allochthonous microbiota. Coastal areas are amongst the most frequent relocation choices, especially in regions where desertification is taking place. A warmer future will likely require looking beyond the use of traditional water quality indicators to protect human health, in order to guarantee that waterways are safe to use for bathing and recreation. Finally, since sand is a complex matrix, an alternative set of microbial standards is necessary to guarantee that the health of beach users is protected from both sand and water contaminants. We need to plan for the future safer use of beaches by adapting regulations to a climate-changing world.
  • Berthelsen, Hanne; Hakanen, Jari J.; Westerlund, Hugo (2018)
    Aim This study aims at investigating the nomological validity of the Copenhagen Psychosocial Questionnaire (COPSOQ II) by using an extension of the Job Demands-Resources (JD-R) model with aspects of work ability as outcome. Material and methods The study design is cross-sectional. All staff working at public dental organizations in four regions of Sweden were invited to complete an electronic questionnaire (75% response rate, n = 1345). The questionnaire was based on COPSOQ II scales, the Utrecht Work Engagement scale, and the one-item Work Ability Score in combination with a proprietary item. The data was analysed by Structural Equation Modelling. Results This study contributed to the literature by showing that: A) The scale characteristics were satisfactory and the construct validity of COPSOQ instrument could be integrated in the JD-R framework; B) Job resources arising from leadership may be a driver of the two processes included in the JD-R model; and C) Both the health impairment and motivational processes were associated with WA, and the results suggested that leadership may impact WA, in particularly by securing task resources. Conclusion In conclusion, the nomological validity of COPSOQ was supported as the JD-R model can be operationalized by the instrument. This may be helpful for transferral of complex survey results and work life theories to practitioners in the field.
  • Larsson, D. G. Joakim; Andremont, Antoine; Bengtsson-Palme, Johan; Brandt, Kristian Koefoed; Husman, Ana Maria de Roda; Fagerstedt, Patriq; Fick, Jerker; Flach, Carl-Fredrik; Gaze, William H.; Kuroda, Makoto; Kvint, Kristian; Laxminarayan, Ramanan; Manaia, Celia M.; Nielsen, Kaare Magne; Plant, Laura; Ploy, Marie-Cecile; Segovia, Carlos; Simonet, Pascal; Smalla, Kornelia; Snape, Jason; Topp, Edward; van Hengel, Arjon J.; Verner-Jeffreys, David W.; Virta, Marko P. J.; Wellington, Elizabeth M.; Wernersson, Ann-Sofie (2018)
    There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.(1)
  • Rosendahl, Sarah Victoria; Anturaniemi (o.s. Roine), Johanna; Vuori, Kristiina A.; Moore, Robin; Hemida, Manal; Hielm-Bjorkman, Anna (2022)
    Obtaining correct amounts of essential elements, and avoiding toxic metals are key factors in dog health. Through analyzing major and trace elements in hair and blood of 50 healthy companion dogs using ICP-MS, we study their associations with dog characteristics and diet, hypothesizing that eating the same diet long-term results in strong correlations between hair and blood element concentrations, and that dog characteristics and diet affect element status. The correlation between hair and blood was significant for Hg (R = 0.601, p = 0.000) and Pb (R = 0.384, p = 0.010). The following associations were significant (p < 0.05): Dark hair had higher Ca and Mg compared to light hair. Females had higher hair Zn, blood Mn, and blood As compared to males. Blood Mn and Se increased, while blood Pb decreased with age. Raw diet fed dogs had higher hair Zn and Se compared to dry or mixed diet fed dogs, and lower blood Mn compared to dry diet fed dogs. Dry and mixed diet fed dogs had higher blood Cd compared to raw diet fed dogs. Mixed diet fed dogs had higher hair Ca and Mg compared to raw or dry diet fed dogs, and higher hair Pb compared to dry diet fed dogs. Wild game consumption was associated with higher blood Pb, and rice consumption with higher blood As. In conclusion, hair provides an alternative for assessing Hg and Pb exposure, and major and trace elements status is affected by hair color, sex, age, and diet.
  • Dickel, Franziska; Munch, Daniel; Amdam, Gro Vang; Mappes, Johanna; Freitak, Dalial (2018)
    Recent studies of honeybees and bumblebees have examined combinatory effects of different stressors, as insect pollinators are naturally exposed to multiple stressors. At the same time the potential influences of simultaneously occurring agricultural agents on insect pollinator health remain largely unknown. Due to different farming methods, and the drift of applied agents and manure, pollinators are most probably exposed to insecticides but also bacteria from organic fertilizers at the same time. We orally exposed honeybee workers to sub-lethal doses of the insecticide thiacloprid and two strains of the bacterium Enterococcus faecalis, which can occur in manure from farming animals. Our results show that under laboratory conditions the bees simultaneously exposed to the a bacterium and the pesticide thiacloprid thiacloprid had significant higher survival rates 11 days post exposure than the controls, which surprisingly showed the lowest survival. Bees that were exposed to diet containing thiacloprid showed decreased food intake. General antibacterial activity is increased by the insecticide and the bacteria, resulting in a higher immune response observed in treated individuals compared to control individuals. We thus propose that caloric restriction through behavioural and physiological adaptations may have mediated an improved survival and stress resistance in our tests. However, the decreased food consumption could in long-term also result in possible negative effects at colony level. Our study does not show an additive negative impact of sub-lethal insecticide and bacteria doses, when tested under laboratory conditions. In contrast, we report seemingly beneficial effects of simultaneous exposure of bees to agricultural agents, which might demonstrate a surprising biological capacity for coping with stressors, possibly through hormetic regulation.
  • Haapasaari, Päivi; Ignatius, Suvi; Pihlajamaki, Mia; Bryhn, Andreas; Sarkki, Simo; Tuomisto, Jouni T.; Ronkainen, Lauri; Lehikoinen, Annukka; Assmuth, Timo; Romakkaniemi, Atso; Peltonen, Heikki; Kuikka, Sakari (2021)
    The implementation challenge of ecosystem-based (fisheries) management (EB(F)M) has entailed calls for integrated governance (IG) approaches in the marine field. We arranged an expert workshop to study the preconditions and applicability of IG, and to suggest how IG could be arranged in practice. Focusing on the management of the dioxin problem shared by the herring and salmon fisheries in the Baltic Sea, and using a coupled ‘insight network’- SWOT (strengths, weaknesses, opportunities, threats) methodology, we evaluated two scenarios: 1) IG of herring and salmon fisheries to benefit from collaboration between these fisheries that suffer from the same problem, and 2) IG between the fisheries sector and the food/public health sector to incorporate food safety in fisheries governance. Our results demonstrate that a variety of societal, political, institutional, operational, instrumental, and biological factors affect the applicability of IG in marine contexts, and work as preconditions for IG. While societal needs for IG were obvious in our case, as major challenges for it we identified the competing cross-sectoral objectives, path dependencies, and limitations of experts to think and work across fields. The study suggests that establishing an IG framework by adding new aspects upon the current governance structures may be easier to accept and adapt to, than creating new strategic or advisory bodies or other new capacities. Viewing IG as a framework for understanding cross-sectoral issues instead of one that requires a defined level and form of integrated assessment and management may be a way towards social learning, and thereby towards the implementation of more sophisticated, open and broad EB(F)M frameworks.
  • Savi, Flavia; Nemitz, Eiko; Coyle, Mhairi; Aitkenhead, Matt; Frumau, Kfa; Gerosa, Giacomo; Finco, Angelo; Gruening, Carten; Goded, Ignacio; Loubet, Benjamin; Stella, Patrick; Ruuskanen, Taina; Weidinger, T.; Horvath, L.; Zenone, Terenzio; Fares, Silvano (2020)
    Tropospheric ozone (O-3) is probably the air pollutant most damaging to vegetation. Understanding how plants respond to O(3)pollution under different climate conditions is of central importance for predicting the interactions between climate change, ozone impact and vegetation. This work analyses the effect of O(3)fluxes on net ecosystem productivity (NEP), measured directly at the ecosystem level with the eddy covariance (EC) technique. The relationship was explored with artificial neural networks (ANNs), which were used to model NEP using environmental and phenological variables as inputs in addition to stomatal O(3)uptake in Spring and Summer, when O(3)pollution is expected to be highest. A sensitivity analysis allowed us to isolate the effect of O-3, visualize the shape of the O-3-NEP functional relationship and explore how climatic variables affect NEP response to O-3. This approach has been applied to eleven ecosystems covering a range of climatic areas. The analysis highlighted that O(3)effects over NEP are highly non-linear and site-specific. A significant but small NEP reduction was found during Spring in a Scottish shrubland (-0.67%), in two Italian forests (up to -1.37%) and during Summer in a Californian orange orchard (-1.25%). Although the overall seasonal effect of O(3)on NEP was not found to be negative for the other sites, with episodic O(3)detrimental effect still identified. These episodes were correlated with meteorological variables showing that O(3)damage depends on weather conditions. By identifying O(3)damage under field conditions and the environmental factors influencing to that damage, this work provides an insight into O(3)pollution, climate and weather conditions.
  • Verbrugge, Laura N. H.; Dawson, Murray; Gettys, Lyn A.; Leuven, Rob S. E. W.; Marchante, Helia; Marchante, Elizabete; Nummi, Petri; Rutenfrans, Annerie H. M.; Schneider, Katrin; Vanderhoeven, Sonia (2021)
    Increasing public awareness is a prerequisite for successful management of invasive alien species (IAS). Environmental education can play an important role in this process by providing relevant learning outcomes and experiences for youth and students, as well as professionals in different sectors associated with introduction pathways or who are involved in mitigation and eradication of IAS. This paper responds to the urgent call for the inclusion of the IAS topic in education through the development, implementation and evaluation of novel and user-friendly educational materials. The aim of this paper is to describe best practices in IAS education and to share the lessons learned from eight educational projects from seven different countries. We discuss four challenges for IAS education, related to (1) inconsistent and ambiguous terminology, (2) communicating risk, (3) implementation of education materials, and (4) evaluation of learning effects. Examples of best practices are the use of smartphone applications and gaming elements, place-based education and exhibitions. We also note the importance of open access publishing of education materials to make them easily available. We intend this discussion to serve as a source of inspiration to researchers, science communicators and teachers and to spur the development of new teaching materials worldwide.
  • Haukka, Anna; Heikkinen, Anna Maria; Haukka, Jari; Kaila, Minna (2020)
    Objectives: The individualised recall interval (IRI) is part of the oral health examination. This observational, register-based study aimed to explore how oral health indices DMFT (decayed, missing, filled teeth), DT (decayed teeth), CPI (Community Periodontal Index, maximum value of individual was used) and number of teeth are associated with IRI for adults. Methods: Oral health examination includes an assessment of all oral tissues, diagnosis, a treatment plan and assessment and a determination of the interval before the next assessment. It is called the IRI. This cross-sectional study population included 42,533 adults (age range 18-89 years), who had visited for an oral health examination during 2009, provided by the Helsinki City Social Services and Health Care. The recall interval was categorised into an ordinal scale (0-12, 13-24, 25-36 and 37-60 months) and was modelled using a proportional odds model. ORs less than one indicated a shorter recall interval. Results: Recall interval categories in the study population were 0-12 months (n = 4,569; 11%), 13-24 months (n = 23,732; 56%), 25-36 months (n = 12,049; 28%), and 37-60 months (n = 2,183; 5%). The results of statistical models clearly showed an association between the length of recall intervals and oral health indices. In all models, higher values of DMFT, DT and CPI indicated a shorter recall interval. The number of teeth were not so relevant. The association was not influenced when different combinations of other predictors (age, gender, socioeconomic status, chronic diseases) were included in the model. The severity of periodontitis predicted a short recall interval, for example, in the Model 1, CPI maximum value 4 was OR = 0.35 (95% confidence interval 0.31-0.40). Conclusions: The oral health indices showed a clear association with the length of the IRI. Poor oral health reduced IRI. The indices provide information about the amount of oral health prevention required and are useful to health organisations.
  • Rabiei, Sepideh; Mohebbi, Simin Z.; Yazdani, Reza; Virtanen, Jorma I. (2014)
  • Lopez, Fernando; Mäkitie, Antti; de Bree, Remco; Franchi, Alessandro; de Graaf, Pim; Hernandez-Prera, Juan C.; Strojan, Primoz; Zidar, Nina; Flezar, Margareta Strojan; Rodrigo, Juan P.; Rinaldo, Alessandra; Centeno, Barbara A.; Ferlito, Alfio (2021)
    The diagnosis is the art of determining the nature of a disease, and an accurate diagnosis is the true cornerstone on which rational treatment should be built. Within the workflow in the management of head and neck tumours, there are different types of diagnosis. The purpose of this work is to point out the differences and the aims of the different types of diagnoses and to highlight their importance in the management of patients with head and neck tumours. Qualitative diagnosis is performed by a pathologist and is essential in determining the management and can provide guidance on prognosis. The evolution of immunohistochemistry and molecular biology techniques has made it possible to obtain more precise diagnoses and to identify prognostic markers and precision factors. Quantitative diagnosis is made by the radiologist and consists of identifying a mass lesion and the estimation of the tumour volume and extent using imaging techniques, such as CT, MRI, and PET. The distinction between the two types of diagnosis is clear, as the methodology is different. The accurate establishment of both diagnoses plays an essential role in treatment planning. Getting the right diagnosis is a key aspect of health care, and it provides an explanation of a patient's health problem and informs subsequent decision. Deep learning and radiomics approaches hold promise for improving diagnosis.
  • Hijazi, Ziad; Lindahl, Bertil; Oldgren, Jonas; Andersson, Ulrika; Lindback, Johan; Granger, Christopher B.; Alexander, John H.; Gersh, Bernard J.; Hanna, Michael; Harjola, Veli-Pekka; Hylek, Elaine M.; Lopes, Renato D.; Siegbahn, Agneta; Wallentin, Lars (2017)
    Background--Cardiac biomarkers are independent risk markers in atrial fibrillation, and the novel biomarker-based ABC stroke score (age, biomarkers, and clinical history of prior stroke) was recently shown to improve the prediction of stroke risk in patients with atrial fibrillation. Our aim was to investigate the short-term variability of the cardiac biomarkers and evaluate whether the ABC stroke risk score provides a stable short- term risk estimate. Methods and Results--According to the study protocol, samples were obtained at entry and also at 2 months in 4796 patients with atrial fibrillation followed for a median of 1.8 years in the ARISTOTLE (Apixaban for Reduction in Stroke and Other Thromboembolic Events in Atrial Fibrillation) trial. Cardiac troponin I, cardiac troponin T, and N-terminal pro-B-type natriuretic peptide were measured with high-sensitivity immunoassays. Associations with outcomes were evaluated by Cox regression. C indices and calibration plots were used to evaluate the ABC stroke score at 2 months. The average changes in biomarker levels during 2 months were small ( median change cardiac troponin T +2.8%, troponin I +2.0%, and N-terminal pro-B-type natriuretic peptide +13.5%) and within-subject correlation was high ( all >= 0.82). Repeated measurement of cardiac biomarkers provided some incremental prognostic value for mortality but not for stroke when combined with clinical risk factors and baseline levels of the biomarkers. Based on 8702 person-years of follow-up and 96 stroke/systemic embolic events, the ABC stroke score at 2 months achieved a similar C index of 0.70 (95% CI, 0.65-0.76) as compared with 0.70 (95% CI, 0.65-0.75) at baseline. The ABC stroke score remained well calibrated using predefined risk classes. Conclusions--In patients with stable atrial fibrillation, the variability of the cardiac biomarkers and the biomarker- based ABC stroke score during 2 months are small. The prognostic information by the ABC stroke score remains consistent and well calibrated with similar good predictive performance if patients are retested after 2 months. Clinical Trial Registration --URL: Unique identifier: NCT00412984.
  • Ndika, Joseph; Seemab, Umair; Poon, Wing-Lam; Fortino, Vittorio; El-Nezami, Hani; Karisola, Piia; Alenius, Harri (2019)
    After over a decade of nanosafety research, it is indisputable that the vast majority of nano-sized particles induce a plethora of adverse cellular responses - the severity of which is linked to the material's physicochemical properties. Differentiated THP-1 cells were previously exposed for 6 h and 24 h to silver, titanium dioxide, and zinc oxide nanoparticles at the maximum molar concentration at which no more than 15% cellular cytotoxicity was observed. All three nanoparticles differed in extent of induction of biological pathways corresponding to immune response signaling and metal ion homeostasis. In this study, we integrated gene and miRNA expression profiles from the same cells to propose miRNA biomarkers of adverse exposure to metal-based nanoparticles. We employed RNA sequencing together with a quantitative strategy that also enables analysis of the overlooked repertoire of length and sequence miRNA variants called isomiRs. Whilst only modest changes in expression were observed within the first 6 h of exposure, the miRNA/isomiR (miR) profiles of each nanoparticle were unique. Via canonical correlation and pathway enrichment analyses, we identified a co-regulated miR-mRNA cluster, predicted to be highly relevant for cellular response to metal ion homeostasis. These miRs were annotated to be canonical or variant isoforms of hsa-miR-142-5p, -342-3p, -5100, -6087, -6894-3p, and -7704. Hsa-miR-5100 was differentially expressed in response to each nanoparticle in both the 6 h and 24 h exposures. Taken together, this co-regulated miR-mRNA cluster could represent potential biomarkers of sub-toxic metal-based nanoparticle exposure.
  • Kinaret, Pia Anneli Sofia; Serra, Angela; Federico, Antonio; Kohonen, Pekka; Nymark, Penny; Liampa, Irene; Ha, My Kieu; Choi, Jang-Sik; Jagiello, Karolina; Sanabria, Natasha; Melagraki, Georgia; Cattelani, Luca; Fratello, Michele; Sarimveis, Haralambos; Afantitis, Antreas; Yoon, Tae-Hyun; Gulumian, Mary; Grafström, Roland; Puzyn, Tomasz; Greco, Dario (2020)
    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.
  • Lantta, Tella; Kontio, Raija; Daffern, Michael; Adams, Clive E.; Valimaki, Maritta (2016)
    Purpose: This paper aims to explore the acceptability of Dynamic Appraisal of Situational Aggression (DASA) from the perspective of patients, its actual use by mental health nurses, and the predictive validity of the DASA instrument. Methods: A feasibility study design incorporating quantitative and qualitative components was used. The study was conducted in three mental health inpatient units at three hospitals in southern Finland. Quantitative data were used to explore demand (nurses' actual use of the DASA), limited efficacy (predictive validity), and acceptability (measured through patients' participation in the project). Qualitative data were collected to enhance the understanding of acceptability by describing patients' perceptions of the strengths and weaknesses of the DASA. Results: Nurses used the DASA for most patient assessments. The predictive validity of the DASA was outstanding or excellent, depending on the type of aggression predicted, although the patient recruitment ratio was low. Patients reported both strengths and weaknesses of the DASA, providing complementary information regarding the instrument's acceptability and clinical application. Conclusion: The DASA accurately predicts inpatient aggression. The patients' preferences and concerns regarding risk assessment have been noted. More patient involvement in risk assessment research and violence prevention efforts is required.