967 resultados para Extraction methods


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During the last decade, biomedicine has witnessed a tremendous development. Large amounts of experimental and computational biomedical data have been generated along with new discoveries, which are accompanied by an exponential increase in the number of biomedical publications describing these discoveries. In the meantime, there has been a great interest with scientific communities in text mining tools to find knowledge such as protein-protein interactions, which is most relevant and useful for specific analysis tasks. This paper provides a outline of the various information extraction methods in biomedical domain, especially for discovery of protein-protein interactions. It surveys methodologies involved in plain texts analyzing and processing, categorizes current work in biomedical information extraction, and provides examples of these methods. Challenges in the field are also presented and possible solutions are discussed.

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To date, more than 16 million citations of published articles in biomedical domain are available in the MEDLINE database. These articles describe the new discoveries which accompany a tremendous development in biomedicine during the last decade. It is crucial for biomedical researchers to retrieve and mine some specific knowledge from the huge quantity of published articles with high efficiency. Researchers have been engaged in the development of text mining tools to find knowledge such as protein-protein interactions, which are most relevant and useful for specific analysis tasks. This chapter provides a road map to the various information extraction methods in biomedical domain, such as protein name recognition and discovery of protein-protein interactions. Disciplines involved in analyzing and processing unstructured-text are summarized. Current work in biomedical information extracting is categorized. Challenges in the field are also presented and possible solutions are discussed.

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The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.

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Introdução: O processo alveolar é o conjunto de osso que se encontra em redor da raiz do dente. Este osso é sensível a uma variedade de fatores ambientais e fisiológicos que influenciam a sua integridade e o seu funcionamento. Como tal, a sua formação assim como a sua preservação é dependente da presença contínua do dente. A reabsorção do processo alveolar após extração dentária é uma consequência natural e fisiológica indesejável, que pode dificultar a colocação de um implante dentário na posição desejada. Com o aumento cada vez mais das demandas estéticas em medicina dentária, torna-se, portanto, necessário prevenir que a reabsorção óssea provoque este defeito na arcada dentária. Objetivos: Realizar uma revisão bibliográfica sobre as várias técnicas e materiais para preservação do rebordo alveolar, a fim de prevenir ou minimizar a reabsorção alveolar após extração dentária. Material e Métodos: A pesquisa foi realizada nas bases de dados Pubmed, B-on e Scielo, não foi aplicado nenhum limite temporal, e os critérios de inclusão foram artigos em língua inglesa e portuguesa. Num total de 164 artigos, selecionaram-se 82 estritamente relacionados com o tema. Os artigos excluídos desviavam-se do objetivo do trabalho ou eram inconclusivos. Selecionaram-se, também, capítulos do livro Clinical Periodontology and Implant Dentistry Volume 1 e 2, dos autores Niklaus P.Lang e Jan Lindhe. Desenvolvimento: De modo a compreender como o processo alveolar reabsorve, deve-se ter em conta as várias técnicas que se podem realizar para permitir uma boa quantidade de osso remanescente na arcada adequada a cada caso para uma possível reabilitação. As técnicas de preservação do osso alveolar após extração passam pela realização de técnicas cirúrgicas minimamente invasivas, estabilização do coágulo pelo princípio da cicatrização por primeira intenção usando membranas ou retalhos, preenchimento do alvéolo dentário com materiais de enxerto ou substitutos ósseos, terapias combinadas com a colocação de implantes imediatos e o recurso a células e fatores de crescimento. Conclusão: A preservação alveolar tem grande importância para uma posterior reabilitação oral com implantes com maior quantidade de osso disponível do que quando não é feita qualquer tipo de preservação. A extração das peças dentárias deve ser feita com cuidado para preservar ao máximo ou não danificar as superfícies ósseas remanescentes. É aconselhado que o encerramento da ferida seja por primeira intenção e que proporcione estabilidade ao coágulo, podendo ser usado retalhos ou mesmo membranas. O uso de enxertos ósseos tem uma importante função de proporcionar uma matriz para o coágulo se formar e promover o processo de cicatrização. O método de implante imediato, para além de ser bastante usado, tem como finalidade o conforto para o paciente de não ser submetido a uma posterior cirurgia para colocação do mesmo e, simultaneamente, mantem a estabilidade dos tecidos moles. Ainda uma técnica menos usada é com células e fatores de crescimento que proporciona uma cicatrização mais rápida e um aumento do potencial regenerativo dos tecidos.

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In this dissertation, there are developed different analytical strategies to discover and characterize mammalian brain peptides using small amount of tissues. The magnocellular neurons of rat supraoptic nucleus in tissue and cell culture served as the main model to study neuropeptides, in addition to hippocampal neurons and mouse embryonic pituitaries. The neuropeptidomcis studies described here use different extraction methods on tissue or cell culture combined with mass spectrometry (MS) techniques, matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). These strategies lead to the identification of multiple peptides from the rat/mouse brain in tissue and cell cultures, including novel compounds One of the goals in this dissertation was to optimize sample preparations on samples isolated from well-defined brain regions for mass spectrometric analysis. Here, the neuropeptidomics study of the SON resulted in the identification of 85 peptides, including 20 unique peptides from known prohormones. This study includes mass spectrometric analysis even from individually isolated magnocellular neuroendocrine cells, where vasopressin and several other peptides are detected. At the same time, it was shown that the same approach could be applied to analyze peptides isolated from a similar hypothalamic region, the suprachiasmatic nucleus (SCN). Although there were some overlaps regarding the detection of the peptides in the two brain nuclei, different peptides were detected specific to each nucleus. Among other peptides, provasopressin fragments were specifically detected in the SON while angiotensin I, somatostatin-14, neurokinin B, galanin, and vasoactive-intestinal peptide (VIP) were detected in the SCN only. Lists of peptides were generated from both brain regions for comparison of the peptidome of SON and SCN nuclei. Moving from analysis of magnocellular neurons in tissue to cell culture, the direct peptidomics of the magnocellular and hippocampal neurons led to the detection of 10 peaks that were assigned to previously characterized peptides and 17 peaks that remain unassigned. Peptides from the vasopressin prohormone and secretogranin-2 are attributed to magnocellular neurons, whereas neurokinin A, peptide J, and neurokinin B are attributed to cultured hippocampal neurons. This approach enabled the elucidation of cell-specific prohormone processing and the discovery of cell-cell signaling peptides. The peptides with roles in the development of the pituitary were analyzed using transgenic mice. Hes1 KO is a genetically modified mouse that lives only e18.5 (embryonic days). Anterior pituitaries of Hes1 null mice exhibit hypoplasia due to increased cell death and reduced proliferation and in the intermediate lobe, the cells differentiate abnormally into somatotropes instead of melanotropes. These previous findings demonstrate that Hes1 has multiple roles in pituitary development, cell differentiation, and cell fate. AVP was detected in all samples. Interestingly, somatostatin [92-100] and provasopressin [151-168] were detected in the mutant but not in the wild type or heterozygous pituitaries while somatostatin-14 was detected only in the heterozygous pituitary. In addition, the putative peptide corresponding to m/z 1330.2 and POMC [205-222] are detected in the mutant and heterozygous pituitaries, but not in the wild type. These results indicate that Hes1 influences the processing of different prohormones having possible roles during development and opens new directions for further developmental studies. This research demonstrates the robust capabilities of MS, which ensures the unbiased direct analysis of peptides extracted from complex biological systems and allows addressing important questions to understand cell-cell signaling in the brain.

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Chemical speciation in foodstuffs is of uttermost importance since it is nowadays recognized that both toxicity and bioavailability of an element depend on the chemical form in which the element is present. Regarding arsenic, inorganic species are classified as carcinogenic while organic arsenic, such as arsenobetaine (AsB) or arsenocholine (AsC), is considered less toxic or even non-toxic. Coupling a High Performance Liquid Chromatographer (HPLC) with an Inductively Coupled Plasma Mass Spectrometer (ICP-MS) combines the power of separation of the first with the selectivity and sensitivity of the second. The present work aims at developing a method, using HPLC-ICP-MS technique, to identify and quantify the chemical species of arsenic present in two food matrices, rice and fish. Two extraction methods, ultrasound and microwave, and different settings were studied. The best method was chosen based on recovery percentages. To ensure that no interconversion of species was occurring, individual spikes of each species of arsenic were made in both matrices and recovery rates were calculated. To guaranty accurate results reference material BCR-627 TUNA FISH, containing certified values for AsB and DMA, was analyzed. Chromatographic separation was achieved using an anion exchange column, HAMILTON-PRP X-100, which allowed to separate the four arsenic species for which standards were available (AsB, dimethylarsenic (DMA), arsenite (AsIII), arsenate (AsV). The mobile phase was chosen based on scientific literature and adjusted to laboratory conditions. Different gradients were studied. As a result we verified that the arsenic species present in both matrices were not the same. While in fish 90% of the arsenic present was in the form of arsenobetaine, in rice 80% of arsenic was present as DMA and 20% as inorganic arsenic.

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Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

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Over the past years, ω3 fatty acids, namely EPA and DHA, have been recognized as presenting multiple health benefits. Several studies consider fish oil as the most important source of EPA and DHA. Nowadays, canned fish industry plays a very important role in Portuguese economy. However, expansion of this business brought some environmental concerns due to the high amount of by-products generated. Nevertheless, this problem can be substantially reduced by the recovery of some of the by-product components, diminishing its contamination load and simultaneously obtaining value-added products. This study was born from the growing interest in obtaining new sources of lipids rich in ω3 fatty acids, combined with environmental concerns related to the production of wastes from the fish canning industries, rich in these compounds. It thus intends to evaluate lipid extraction methods in liquid by-products from the fish canning industry, aiming to obtain fractions rich in ω3 fatty acids. Additionally, in a biorefining concept, the protein content of the remaining aqueous fractions was also quantified.

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A produção de biodiesel a partir do óleo de microalgas tem sido demonstrada na literatura usando rotas convencionais, que envolvem a extração dos lipídeos seguida pela sua conversão para ésteres graxos. A extração de lipídeos a partir da biomassa microalgal é uma etapa importante do processo global de produção de biodiesel. Este trabalho teve como objetivo determinar o teor de lipídeos da Chlorella pyrenoidosa bem como o perfil graxo dos diferentes extratos lipídicos. Os métodos de extração utilizados envolveram o uso de ultrassom, agitação magnética e soxhlet na presença dos solventes: clorofórmio:metanol (2:1 v/v) (método de Bligh & Dyer), metanol, clorofórmio, etanol e hexano. Os melhores resultados foram obtidos a partir do método com agitação magnética utilizando clorofórmio:metanol 2:1 (v/v), onde foram extraídos em média de 20 % de lipídeos totais seguido de metanol (17 %), clorofórmio (10,5 %), etanol (7,8 %) e hexano (1,15 %). A presença dos ácidos graxos 14:0, 16:0, 18:1, 18:0, 18:2 e 18:3 foram confirmados pelas análises de cromatografia gasosa. A partir das frações lipídicas extraídas foram realizadas as reações para obtenção dos ésteres graxos utilizando temperatura de 60°C por 4h na presença de 3% de H2SO4 em relação à massa de lipídeos. Os extratos lipídicos foram obtidos usando 100 g de biomassa seca. A partir das frações extraídas com clorofórmio:metanol 2:1 (v/v), metanol e etanol foram produzidos em média 6,40g, 8,98g, 6,98g de ésteres graxos, respectivamente.

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Purpose: To develop liposome formulations containing monoclonal antibody anti-HER2 (MabHer2), and Paclitaxel (PTX). Methods: Seven different liposomal systems containing PTX, or MabHer2 or a combination of PTX and MabHer2 were made using lipid film hydration technique and sonication. The effects of liposome preparation conditions and extraction methods on antibody structure were investigated by polyacrylamide gel electrophoresis and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The characteristics of the liposomes were determined by a zetasizer, while drug-loading efficiency was evaluated by high-performance liquid chromatography. The cytotoxic effect of the liposome formulations was evaluated on MDA-MB-453 (HER2+) and MCF-7 (HER2-) breast cancer cell lines by MTT assay. Results: The antibody was not significantly affected by the stress conditions and the method of extraction. The particle size of liposomes was < 200 nm while the amount of incorporated PTX was 97.6 % for liposome without cationic agent and 98.2 % for those with cationic agent. Recovery of MabHer2 was 94.38 % after extraction. Combined PTX/MabHer2 liposome was more toxic on HER2 overexpressing positive MDA-MB-453 cell line than PTX-loaded liposomes and MabHer2. MabHer2 and combined PTX/MabHer2 liposomes showed no toxic effects on HER2 overexpressing negative MCF-7 cells relative to cationic PTX-loaded liposomes. Conclusions: This results obtained show that PTX can be encapsulated successfully into liposoma systems and that owing to Her2 specific antibody, these systems can be delivered directly to the target cell.

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To analyze the characteristics and predict the dynamic behaviors of complex systems over time, comprehensive research to enable the development of systems that can intelligently adapt to the evolving conditions and infer new knowledge with algorithms that are not predesigned is crucially needed. This dissertation research studies the integration of the techniques and methodologies resulted from the fields of pattern recognition, intelligent agents, artificial immune systems, and distributed computing platforms, to create technologies that can more accurately describe and control the dynamics of real-world complex systems. The need for such technologies is emerging in manufacturing, transportation, hazard mitigation, weather and climate prediction, homeland security, and emergency response. Motivated by the ability of mobile agents to dynamically incorporate additional computational and control algorithms into executing applications, mobile agent technology is employed in this research for the adaptive sensing and monitoring in a wireless sensor network. Mobile agents are software components that can travel from one computing platform to another in a network and carry programs and data states that are needed for performing the assigned tasks. To support the generation, migration, communication, and management of mobile monitoring agents, an embeddable mobile agent system (Mobile-C) is integrated with sensor nodes. Mobile monitoring agents visit distributed sensor nodes, read real-time sensor data, and perform anomaly detection using the equipped pattern recognition algorithms. The optimal control of agents is achieved by mimicking the adaptive immune response and the application of multi-objective optimization algorithms. The mobile agent approach provides potential to reduce the communication load and energy consumption in monitoring networks. The major research work of this dissertation project includes: (1) studying effective feature extraction methods for time series measurement data; (2) investigating the impact of the feature extraction methods and dissimilarity measures on the performance of pattern recognition; (3) researching the effects of environmental factors on the performance of pattern recognition; (4) integrating an embeddable mobile agent system with wireless sensor nodes; (5) optimizing agent generation and distribution using artificial immune system concept and multi-objective algorithms; (6) applying mobile agent technology and pattern recognition algorithms for adaptive structural health monitoring and driving cycle pattern recognition; (7) developing a web-based monitoring network to enable the visualization and analysis of real-time sensor data remotely. Techniques and algorithms developed in this dissertation project will contribute to research advances in networked distributed systems operating under changing environments.

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The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.^

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Background: Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biopsies. There is an urgent need for collection and transport media that would allow faecal sampling at distance from the processing laboratory, obviating the need for same-day DNA extraction recommended by previous studies of freezing and processing methods for stool. We compared the faecal bacterial DNA quality and apparent phylogenetic composition derived using a commercial kit for stool storage and transport (DNA Genotek OMNIgene GUT) with that of freshly extracted samples, 22 from infants and 20 from older adults. Results: Use of the storage vials increased the quality of extracted bacterial DNA by reduction of DNA shearing. When infant and elderly datasets were examined separately, no differences in microbiota composition were observed due to storage. When the two datasets were combined, there was a difference according to a Wilcoxon test in the relative proportions of Faecalibacterium, Sporobacter, Clostridium XVIII, and Clostridium XlVa after 1 week's storage compared to immediately extracted samples. After 2 weeks' storage, Bacteroides abundance was also significantly different, showing an apparent increase from week 1 to week 2. The microbiota composition of infant samples was more affected than that of elderly samples by storage, with significantly higher Spearman distances between paired freshly extracted and stored samples (p

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Microplastics have become ubiquitous pollutants in the marine environment. Ingestion of microplastics by a wide range of marine organisms has been recorded both in laboratory and field studies. Despite growing concern for microplastics, few studies have evaluated their concentrations and distribution in wild populations. Further, there is a need to identify cost-effective standardized methodologies for microplastics extraction and analysis in organisms. In this thesis I present: (i) the results of a multi-scale field sampling to quantify and characterize microplastics occurrence and distribution in 4 benthic marine invertebrates from saltmarshes along the North Adriatic Italian coastal lagoons; (ii) a comparison of the effects and cost-effectiveness of two extraction protocols for microplastics isolation on microfibers and on wild collected organisms; (iii) the development of a novel field- based technique to quantify and characterize the microplastic uptake rates of wild and farmed populations of mussels (Mytilus galloprovincialis) through the analysis of their biodeposits. I found very low and patchy amounts of microplastics in the gastrointestinal tracts of sampled organisms. The omnivorous crab Carcinus aestuarii was the species with the highest amounts of microplastics, but there was a notable variation among individuals. There were no substantial differences between enzymatic and alkaline extraction methods. However, the alkaline extraction was quicker and cheaper. Biodeposit traps proved to be an effective method to estimate mussel ingestion rates. However their performance differed significantly among sites, suggesting that the method, as currently designed, is sensible to local environmental conditions. There were no differences in the ingestion rates of microplastics between farmed and wild mussels. The estimates of microplastic ingestion and the validated procedures for their extraction provide a strong basis for future work on microplastic pollution.

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A relevant problem of polyolefins processing is the presence of volatile and semi-volatile compounds (VOCs and SVOCs) such as linear chains alkanes found out in final products. These VOCs can be detected by customers from the unpleasant smelt and can be an environmental issue, at the same time they can cause negative side effects during process. Since no previously standardized analytical techniques for polymeric matrix are available in bibliography, we have implemented different VOCs extraction methods and gaschromatographic analysis for quali-quantitative studies of such compounds. In literature different procedures can be found including microwave extraction (MAE) and thermo desorption (TDS) used with different purposes. TDS coupled with GC-MS are necessary for the identification of different compounds in the polymer matrix. Although the quantitative determination is complex, the results obtained from TDS/GC-MS show that by-products are mainly linear chains oligomers with even number of carbon in a C8-C22 range (for HDPE). In order to quantify these linear alkanes by-products, a more accurate GC-FID determination with internal standard has been run on MAE extracts. Regardless the type of extruder used, it is difficult to distinguish the effect of the various processes, which in any case entails having a lower-boiling substance content, lower than the corresponding virgin polymer. The two HDPEs studied can be distinguished on the basis of the quantity of analytes found, therefore the production process is mainly responsible for the amount of VOCs and SVOCs observed. The extruder technology used by Sacmi SC allows to obtain a significant reduction in VOCs compared to the conventional screw system. Thus, the result is significantly important as a lower quantity of volatile substances certainly leads to a lower migration of such materials, especially when used for food packaging.